Answers.Body: <p>I had a think about this one and am stumped. I thought there could be a connection with acute oak disease (AOD) or else chronic oak disease (COD), which are emergent infections threatening the population. However, they appear to be fungal and bacterial infections rather than viral.</p>
  <p>Single stranded RNA plant viruses are very common, more so than in mammals, but to achieve the results you are obtaining the trees would need to be really sick if the predominent RNA was viral. Short viral RNAs are produced regularly by viruses as defective RNA and its a major area of research, considering a mechanism of defective interference,</p>
  <p>In context it would be weird if this RNA swamped the tree/plant, you need an actively replicating virus for this stuff to appear. So I don't think its either viral or defective viral RNA.</p>
  <p>The antiviral response in mammals can involve RNase and this could explain your degradation. Essentially, mammals (probably vertebrates) kick-back hard when virus appears. However, I couldn't really find evidence of this in plants.</p>
  <p>I don't think the results you obtained have a clear biological explanation in pathogenesis. The best explanation is it was wet lab-technique, e.g. library construction resulted in overdigestion/fragmentation. The only thing I can suggest is template assembly using a normally distributed plant/oak RNA library.</p>
  <p>I was probably overthinking in forging a link with an emergent (tree) pathogen.</p>
  <hr />
  <p><img src="https://i.sstatic.net/ayKYJ.jpg" alt="enter image description here" />!</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-05T11:36:18.727Z
Answers.Text: Thanks you Michael. Your answer looks fit better with my results.
Answers.UserDisplayName: Adrián P.L.
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-05T11:40:26.990Z
Answers.Text: I will ask to the sequencing company asking them about the library construction. Thank you again
Answers.UserDisplayName: Adrián P.L.
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-05T12:29:59.560Z
Answers.Text: Thanks you are too kind, but emergent viruses is what I do (albeit for humans not plants) and I couldn't get this one to make sense. Ask them for the Agilent library outputs, both good runs.and 50bp run. I've posted an example above.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-07T16:11:20.873Z
Answers.Text: Hi @AdriánP.L. please let us know how you get on here: one way or another we'll get this resolved if not directly via collaboration.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-07T17:05:10.143Z
Answers.Text: Dear @Michael I though It was solved, your answer looks fitting well with the trouble .
Answers.UserDisplayName: Adrián P.L.
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-07T18:16:25.447Z
Answers.Text: Hi @AdriánP.L. that is great news. Thanks for the update, and glad its been worked out.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-05T03:29:16.500Z
Answers.LastActivityDate: 2020-07-05T12:31:34.910Z
Answers.LastEditDate: 2020-07-05T12:31:34.910Z
Answers.UserDisplayName: M__
Body: <p>I performed a blastn search of NGS data against ssRNA database download from Internet, with a expected value 10-4. The size of NGS data reads is of 125 bp.</p>
  <p>I have analyzed the blast results of the libraries. These libraries are from different habitats. The most difficult habitat, oakwood, produced a blast results with a maximum length of 51 bp. These results have a qcov of 100 (in most of the cases).</p>
  <p>I would like to know if these low length sizes comes from degradation?</p>
  <p>Should do  I filter these samples with a length = 125 bp with the aim to obtain results with better quality or with a qcov of 100 is enought to get reliable results?</p>
  <p>Thanks you in advance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-15T10:07:44.923Z
Comments.Text: I think you should maybe rely on the hitscore, because it integrates both overlap length and % of identity. In addition, you may have a look at MMSeqs2 as an alternative to BLAST. It is much faster, and has tutorials to blast ssRNA db such as SILVA (https://github.com/soedinglab/mmseqs2/wiki).
Comments.UserDisplayName: thomas duge de bernonville
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-15T12:37:36.280Z
Comments.Text: What would "better results" mean? What is wrong with what you get now? If your queries have a maximum length of 125, why would you search for >= 125? How can you have a hit with a length greater than your query sequence? Please [edit] your question and clarify.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-29T19:23:26.450Z
Comments.Text: Could you please explain your RNA extraction protocol from field collection to lab?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-29T19:50:38.477Z
Comments.Text: The RNA extraction was extracted with a CTAB kit from tissue plant of different plants species. This plant species comes from the habitat wilder. My concern is that the blast results gave to me hits with a high qcov and pident and low length.
Comments.UserDisplayName: Adrián P.L.
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-30T04:25:07.533Z
Comments.Text: could please give more information? which ssRNA database are you using? and how your reads have been preprocessed (trimmed)?
Comments.UserDisplayName: thomas duge de bernonville
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-30T12:02:51.850Z
Comments.Text: Any chance these hits are viral species? This would provide a clear explanation about the phenomena.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-30T13:07:08.487Z
Comments.Text: yes, this hits must be a viral species, the database was a ssRNA database downloaded from NCBI. Moreover I trimmed the adapters with cutadapt. The problem is that oakwood habitat is the unique habitat that show this phenomena, the other habitats show longer length in the blast results.
Comments.UserDisplayName: Adrián P.L.
Tags: <blast><ngs><blastn>
Title: Blast results filters
ThreadText: # Blast results filters
  
  (Asked by: username_0 on 2020-05-15)
  
  I performed a blastn search of NGS data against ssRNA database download from Internet, with a expected value 10-4. The size of NGS data reads is of 125 bp.
  
  I have analyzed the blast results of the libraries. These libraries are from different habitats. The most difficult habitat, oakwood, produced a blast results with a maximum length of 51 bp. These results have a qcov of 100 (in most of the cases).
  
  I would like to know if these low length sizes comes from degradation?
  
  Should do I filter these samples with a length = 125 bp with the aim to obtain results with better quality or with a qcov of 100 is enought to get reliable results?
  
  Thanks you in advance.
  
  **Tags:** blast, ngs, blastn
  
  > **Comments:**
  > **username_1**: I think you should maybe rely on the hitscore, because it integrates both overlap length and % of identity. In addition, you may have a look at MMSeqs2 as an alternative to BLAST. It is much faster, and has tutorials to blast ssRNA db such as SILVA (https://github.com/soedinglab/mmseqs2/wiki).  
  > **username_2**: What would "better results" mean? What is wrong with what you get now? If your queries have a maximum length of 125, why would you search for >= 125? How can you have a hit with a length greater than your query sequence? Please [edit] your question and clarify.  
  > **username_3**: Could you please explain your RNA extraction protocol from field collection to lab?  
  > **username_0**: The RNA extraction was extracted with a CTAB kit from tissue plant of different plants species. This plant species comes from the habitat wilder. My concern is that the blast results gave to me hits with a high qcov and pident and low length.  
  > **username_1**: could please give more information? which ssRNA database are you using? and how your reads have been preprocessed (trimmed)?  
  > **username_3**: Any chance these hits are viral species? This would provide a clear explanation about the phenomena.  
  > **username_0**: yes, this hits must be a viral species, the database was a ssRNA database downloaded from NCBI. Moreover I trimmed the adapters with cutadapt. The problem is that oakwood habitat is the unique habitat that show this phenomena, the other habitats show longer length in the blast results.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-07-05. Score: 1 | Accepted answer
  
  I had a think about this one and am stumped. I thought there could be a connection with acute oak disease (AOD) or else chronic oak disease (COD), which are emergent infections threatening the population. However, they appear to be fungal and bacterial infections rather than viral.
  
  Single stranded RNA plant viruses are very common, more so than in mammals, but to achieve the results you are obtaining the trees would need to be really sick if the predominent RNA was viral. Short viral RNAs are produced regularly by viruses as defective RNA and its a major area of research, considering a mechanism of defective interference,
  
  In context it would be weird if this RNA swamped the tree/plant, you need an actively replicating virus for this stuff to appear. So I don't think its either viral or defective viral RNA.
  
  The antiviral response in mammals can involve RNase and this could explain your degradation. Essentially, mammals (probably vertebrates) kick-back hard when virus appears. However, I couldn't really find evidence of this in plants.
  
  I don't think the results you obtained have a clear biological explanation in pathogenesis. The best explanation is it was wet lab-technique, e.g. library construction resulted in overdigestion/fragmentation. The only thing I can suggest is template assembly using a normally distributed plant/oak RNA library.
  
  I was probably overthinking in forging a link with an emergent (tree) pathogen.
  
  ---
  
  ![enter image description here](https://i.sstatic.net/ayKYJ.jpg)!
  
  > **Comments:**
  > **username_0**: Thanks you Michael. Your answer looks fit better with my results.  
  > **username_0**: I will ask to the sequencing company asking them about the library construction. Thank you again  
  > **username_3**: Thanks you are too kind, but emergent viruses is what I do (albeit for humans not plants) and I couldn't get this one to make sense. Ask them for the Agilent library outputs, both good runs.and 50bp run. I've posted an example above.  
  > **username_3**: Hi @AdriánP.L. please let us know how you get on here: one way or another we'll get this resolved if not directly via collaboration.  
  > **username_0**: Dear @Michael I though It was solved, your answer looks fitting well with the trouble .  
  > **username_3**: Hi @AdriánP.L. that is great news. Thanks for the update, and glad its been worked out.  
  
  ---
  
  