Answers.Body: <h4>fishing out tp53 RNA-Seq reads</h4>
  <ul>
  <li>go to <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi" rel="nofollow noreferrer">NCBI Taxonomy Browser</a></li>
  <li>put <code>Anas platyrhynchos</code> as a search term</li>
  <li>click on <code>Anas platyrhynchos</code></li>
  <li>on the right you will have a table with <code>SRA Experiments</code>, click on <code>11,679</code></li>
  <li>restrict to <code>RNA</code> and <code>paired</code> on the left</li>
  <li>send it to <code>Run Selector</code></li>
  <li>order it by the <code>Bases</code></li>
  <li>select few top runs, like <code>SRR16082819</code></li>
  </ul>
  <p>Now it depends what is your exact goal. You may (separate approaches):</p>
  <ul>
  <li>get mallard transcriptome as complete as possible, use <code>kallisto</code> just to check that a given pair of FASTQs contains bunch of reads derived from tp53</li>
  <li>use <code>STAR</code> to align it to the genome with the contig containing TP53 gene</li>
  <li>one can also try to fish out the reads out of FASTQ using tp53 cDNA sequence, but this will likely miss i.e. putative alternative 5- &amp; 3-prime part of the gene</li>
  </ul>
  
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Answers.CreationDate: 2024-02-17T15:06:16.473Z
Answers.Text: Thank you for this insightful response! For the last part, could you add more details about this step of alignment against the genome? Namely, how exactly can I confirm the contig containing the TP53 gene is present and identified using `STAR`?
Answers.UserDisplayName: user18959
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Answers.CreationDate: 2024-02-17T16:55:31.320Z
Answers.Text: It is this contig [NW_024009712](https://www.ncbi.nlm.nih.gov/nuccore/NW_024009712) you will have to get both the genome fasta ans GTF annotation from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015476345.1/
Answers.UserDisplayName: darked89
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Answers.CreationDate: 2024-02-17T16:59:39.520Z
Answers.Text: Also you may try to align the above contig to probably more complete chicken genome to get an idea about how good is the annotation of the p53 gene in mallard/is there anything missing.
Answers.UserDisplayName: darked89
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-20T23:25:46.070Z
Answers.Text: Thank you! For clarity, how did you find that contig? Also, strangely the genome fasta file seems to be corrupted in some way (but other files work, e.g. GTF annotation). Is this genome fasta file hosted anywhere else by chance?
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T09:40:26.823Z
Answers.Text: I did find this updated version (from 2023-12-14) of the genome [here](https://ngdc.cncb.ac.cn/gwh/ncbi_assembly/38807/show), but is there any way to confirm that the GFF/GTF file includes TP53?
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T09:54:20.713Z
Answers.Text: download the annotation then: ``` zcat GCF_015476345.1_ZJU1.0_genomic.gff.gz  | grep "gene=TP53;" | more```
Answers.UserDisplayName: darked89
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T09:58:49.330Z
Answers.Text: That works great — thank you! Going to test this all out now
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T10:15:36.587Z
Answers.Text: I tried converting the GFF to GTF using [this method](https://bioinformatics.stackexchange.com/a/18234/18959) but keep hitting into: `KeyError: 'id-LOC110351722'` (perhaps due to "gene_id" key not being present for key-value pairings of the .gtf file) — trying to resolve it, but if you have any thoughts, certainly glad to receive it
Answers.UserDisplayName: user18959
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Answers.CreationDate: 2024-02-21T10:32:20.600Z
Answers.Text: re conversion gff to gtf: this is a separate question. BTW, why you need it?
Answers.UserDisplayName: darked89
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T10:42:13.930Z
Answers.Text: It's part of the nf-core pipeline — it expects annotations in GTF format, but the above link only provides GFF files. I tried using [gff3_ID_generator.py](https://gff3toolkit.readthedocs.io/en/latest/FAQ.html) to generate IDs if the gff file does not have them for every feature, but the error persists
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T11:01:43.597Z
Answers.Text: I think I've found the solution [here](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/) where the larger repo of files are available
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-21T11:07:46.760Z
Answers.Text: Ok. Still, file another question about the gff to gtf conversion of that particular gff file. And it will be helpful if you up vote and accept the answer as a correct one
Answers.UserDisplayName: darked89
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-22T00:38:32.917Z
Answers.Text: Yep, just running and testing the pipeline with the updated fasta and gtf files to determine if TP53 is ultimately found with the nf-core pipeline (which I expect it should) — but these new files keep resulting in the pipeline terminating due to an error somewhere in the files which I'm trying to trace down
Answers.UserDisplayName: user18959
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-04T05:55:57.267Z
Answers.Text: Got it working now. These gtf files have a lot information that needs to be cleaned / corrected (e.g. missing gene IDs), but it appears to now run!
Answers.UserDisplayName: user18959
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Answers.CreationDate: 2024-02-16T10:45:21.553Z
Answers.LastActivityDate: 2024-02-16T10:45:21.553Z
Answers.UserDisplayName: darked89
Body: <p>I have been running <a href="https://nf-co.re/rnaseq/1.4.2/docs/output" rel="nofollow noreferrer">nf-core</a> in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA sequencing data, Salmon is able to provide gene counts in a file named <code>salmon.merged.gene_counts.tsv</code>. This file has essentially all the information I am seeking with all counts associated to a unique gene_id. But, for a large number of these gene_ids where no specific gene_name is known, I would like to further find the corresponding DNA sequence (or corresponding transcript's RNA sequence) for each gene_id. Accordingly, my question is: where can I find the information to map the gene_id to the corresponding nucleotides of the gene's (or original transcript's) sequence?</p>
  <p>(Apologies in advance if my question is missing information or overly simply and I'm overlooking something obvious — I am quite new to this all.)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-15T12:18:05.737Z
Comments.Text: Which species? Also:can you provide any examples of `gene_ids` you have problems with?
Comments.UserDisplayName: darked89
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-15T12:33:52.073Z
Comments.Text: Anas platyrhynchos (mallard) — I'm trying to actually do the inverse problem and check if [TP53](https://www.ncbi.nlm.nih.gov/gene/119714806/) is present as one of the `gene_ids`. Looking at [related data from https://midb.pnb.uconn.edu/](https://midb.pnb.uconn.edu/basic_search_php2.php?species_var=Anas+platyrhynchos+platyrhynchos&gene=TP53&gene_class=all), this gene seems to be missing there as well
Comments.UserDisplayName: user18959
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-15T12:59:55.703Z
Comments.Text: re TP53: if one search for p53 gene here: https://www.ensembl.org/Anas_platyrhynchos/Info/Index I do not see the TP53 itself, just the genes binding to it, or downstream targets. If the genome is incomplete/full of gaps then tp53 may be missing from annotation. I guess not just in ENSEMBL but from other genome assembly based as well.
Comments.UserDisplayName: darked89
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-15T13:26:54.127Z
Comments.Text: If you look at the orthologues of human TP53 (ENSEMBL), you can find them in chicken, Kakapo, Zebra finch plus a bunch of reptiles. While this is not an ultimate proof that TP53 does exist in your duck, I would expect that some duck RNA-Seq may contain at least fragments of TP53.
Comments.UserDisplayName: darked89
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-15T23:29:14.457Z
Comments.Text: Thank you for sharing these thoughts, @darked89. I suppose my simple question is: what is the best way to check the duck RNAseq data for any fragments of TP53? Any specific insights on methods and files to utilize would be helpful!
Comments.UserDisplayName: user18959
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-16T04:05:25.837Z
Comments.Text: Additionally, out of curiosity, how is it that the [TP53 gene is available on NCBI](https://www.ncbi.nlm.nih.gov/gene/119714806/) but unavailable in Ensembl's automated curation pipeline?
Comments.UserDisplayName: user18959
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-16T08:35:52.977Z
Comments.Text: re ENSEMBL mallard tp53: from the NCBI there is a link to [ENSEMBL rapid](https://rapid.ensembl.org/Anas_platyrhynchos_GCA_015476345.1/Gene/Summary?g=ENSAPLG00030005532;r=JACGAL010000063.1:128466-138874). Could be there are two mallard assemblies or at least two versions?
Comments.UserDisplayName: darked89
Tags: <rna-seq><gene-expression><transcriptome><star><salmon>
Title: After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
ThreadText: # After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
  
  (Asked by: username_0 on 2024-02-15)
  
  I have been running [nf-core](https://nf-co.re/rnaseq/1.4.2/docs/output) in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA sequencing data, Salmon is able to provide gene counts in a file named `salmon.merged.gene_counts.tsv`. This file has essentially all the information I am seeking with all counts associated to a unique gene\_id. But, for a large number of these gene\_ids where no specific gene\_name is known, I would like to further find the corresponding DNA sequence (or corresponding transcript's RNA sequence) for each gene\_id. Accordingly, my question is: where can I find the information to map the gene\_id to the corresponding nucleotides of the gene's (or original transcript's) sequence?
  
  (Apologies in advance if my question is missing information or overly simply and I'm overlooking something obvious — I am quite new to this all.)
  
  **Tags:** rna-seq, gene-expression, transcriptome, star, salmon
  
  > **Comments:**
  > **username_1**: Which species? Also:can you provide any examples of `gene_ids` you have problems with?  
  > **username_0**: Anas platyrhynchos (mallard) — I'm trying to actually do the inverse problem and check if [TP53](https://www.ncbi.nlm.nih.gov/gene/119714806/) is present as one of the `gene_ids`. Looking at [related data from https://midb.pnb.uconn.edu/](https://midb.pnb.uconn.edu/basic_search_php2.php?species_var=Anas+platyrhynchos+platyrhynchos&gene=TP53&gene_class=all), this gene seems to be missing there as well  
  > **username_1**: re TP53: if one search for p53 gene here: https://www.ensembl.org/Anas_platyrhynchos/Info/Index I do not see the TP53 itself, just the genes binding to it, or downstream targets. If the genome is incomplete/full of gaps then tp53 may be missing from annotation. I guess not just in ENSEMBL but from other genome assembly based as well.  
  > **username_1**: If you look at the orthologues of human TP53 (ENSEMBL), you can find them in chicken, Kakapo, Zebra finch plus a bunch of reptiles. While this is not an ultimate proof that TP53 does exist in your duck, I would expect that some duck RNA-Seq may contain at least fragments of TP53.  
  > **username_0**: Thank you for sharing these thoughts, @username_1. I suppose my simple question is: what is the best way to check the duck RNAseq data for any fragments of TP53? Any specific insights on methods and files to utilize would be helpful!  
  > **username_0**: Additionally, out of curiosity, how is it that the [TP53 gene is available on NCBI](https://www.ncbi.nlm.nih.gov/gene/119714806/) but unavailable in Ensembl's automated curation pipeline?  
  > **username_1**: re ENSEMBL mallard tp53: from the NCBI there is a link to [ENSEMBL rapid](https://rapid.ensembl.org/Anas_platyrhynchos_GCA_015476345.1/Gene/Summary?g=ENSAPLG00030005532;r=JACGAL010000063.1:128466-138874). Could be there are two mallard assemblies or at least two versions?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-02-16. Score: 1 | Accepted answer
  
  #### fishing out tp53 RNA-Seq reads
  
  * go to [NCBI Taxonomy Browser](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)
  * put `Anas platyrhynchos` as a search term
  * click on `Anas platyrhynchos`
  * on the right you will have a table with `SRA Experiments`, click on `11,679`
  * restrict to `RNA` and `paired` on the left
  * send it to `Run Selector`
  * order it by the `Bases`
  * select few top runs, like `SRR16082819`
  
  Now it depends what is your exact goal. You may (separate approaches):
  
  * get mallard transcriptome as complete as possible, use `kallisto` just to check that a given pair of FASTQs contains bunch of reads derived from tp53
  * use `STAR` to align it to the genome with the contig containing TP53 gene
  * one can also try to fish out the reads out of FASTQ using tp53 cDNA sequence, but this will likely miss i.e. putative alternative 5- & 3-prime part of the gene
  
  > **Comments:**
  > **username_0**: Thank you for this insightful response! For the last part, could you add more details about this step of alignment against the genome? Namely, how exactly can I confirm the contig containing the TP53 gene is present and identified using `STAR`?  
  > **username_1**: It is this contig [NW_024009712](https://www.ncbi.nlm.nih.gov/nuccore/NW_024009712) you will have to get both the genome fasta ans GTF annotation from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015476345.1/  
  > **username_1**: Also you may try to align the above contig to probably more complete chicken genome to get an idea about how good is the annotation of the p53 gene in mallard/is there anything missing.  
  > **username_0**: Thank you! For clarity, how did you find that contig? Also, strangely the genome fasta file seems to be corrupted in some way (but other files work, e.g. GTF annotation). Is this genome fasta file hosted anywhere else by chance?  
  > **username_0**: I did find this updated version (from 2023-12-14) of the genome [here](https://ngdc.cncb.ac.cn/gwh/ncbi_assembly/38807/show), but is there any way to confirm that the GFF/GTF file includes TP53?  
  > **username_1**: download the annotation then: ``` zcat GCF_015476345.1_ZJU1.0_genomic.gff.gz  | grep "gene=TP53;" | more```  
  > **username_0**: That works great — thank you! Going to test this all out now  
  > **username_0**: I tried converting the GFF to GTF using [this method](https://bioinformatics.stackexchange.com/a/18234/18959) but keep hitting into: `KeyError: 'id-LOC110351722'` (perhaps due to "gene_id" key not being present for key-value pairings of the .gtf file) — trying to resolve it, but if you have any thoughts, certainly glad to receive it  
  > **username_1**: re conversion gff to gtf: this is a separate question. BTW, why you need it?  
  > **username_0**: It's part of the nf-core pipeline — it expects annotations in GTF format, but the above link only provides GFF files. I tried using [gff3_ID_generator.py](https://gff3toolkit.readthedocs.io/en/latest/FAQ.html) to generate IDs if the gff file does not have them for every feature, but the error persists  
  > **username_0**: I think I've found the solution [here](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/) where the larger repo of files are available  
  > **username_1**: Ok. Still, file another question about the gff to gtf conversion of that particular gff file. And it will be helpful if you up vote and accept the answer as a correct one  
  > **username_0**: Yep, just running and testing the pipeline with the updated fasta and gtf files to determine if TP53 is ultimately found with the nf-core pipeline (which I expect it should) — but these new files keep resulting in the pipeline terminating due to an error somewhere in the files which I'm trying to trace down  
  > **username_0**: Got it working now. These gtf files have a lot information that needs to be cleaned / corrected (e.g. missing gene IDs), but it appears to now run!  
  
  ---
  
  