Answers.Body: <p>Possible?  Sure.  Your biggest problem is that 10x is expecting barcodes from its whitelist.  I used to alter the python scripts to accept a 'new' kind of chemistry where the barcodes and umi lengths matched what I had, but I found that my modifications stopped working when the version updated,  and I couldn't figure it out, so I started modifying fastqs instead.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-17T21:26:59.933Z
Answers.Text: Do you mind sharing the altered code? And how do you modify the fastqs?
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-18T02:03:05.893Z
Answers.Text: My modifications didn't work, and I strongly recommend not changing code like that unless you understand what you are doing.  As to changing the fastqs, you have to understand the format you've got, and what format you want.  I use umi_tools to identify the barcodes and their one-offs, and use that list to make replacements.
Answers.UserDisplayName: swbarnes2
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-17T20:35:40.230Z
Answers.LastActivityDate: 2020-02-17T20:35:40.230Z
Answers.UserDisplayName: swbarnes2
Body: <p>I'm trying to use cellranger to <code>mkfastq</code> and then <code>count</code> and <code>aggregate</code> single-cell data. This data was not generated using 10x Genomics RNASeq. </p>
  
  <p>When I run <code>count</code>, cellranger fails to auto id the chemistry and crashes out. Is it possible to wrangle the data into the cellranger method or should I look elsewhere. I'd ideally like to use the same method for all my single-cell data but not all of it is 10x.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-17T16:18:30.257Z
Comments.Text: Hi Yuriy, could you tell us what how you generated the RNAseq data? That might be important. Also what species/problem you are working with?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-17T20:25:05.530Z
Comments.Text: How do the fastq files that belong to a given sample look like, I mean how are they named? Can you share the `ls` output of a given sample directory?
Comments.UserDisplayName: haci
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-20T04:58:30.383Z
Comments.Text: Perhaps [STARsolo](https://github.com/alexdobin/STAR/blob/2.7.3a/docs/STARsolo.md) is worth looking into.
Comments.UserDisplayName: merv
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-24T09:23:07.197Z
Comments.Text: Hi, It is Smart-Seq2 data that I am hoping to overlap with some 10x data. Regarding the fastq I had to use the mkfastq command. For each sample, I have _R1 _R2 _I1 _I2 files. The naming consists of the sample name, the clone, the lane and the read.
Comments.UserDisplayName: Yuriy Grabovsky
Tags: <single-cell><cellranger>
Title: Using cellranger for non-10x data
ThreadText: # Using cellranger for non-10x data
  
  (Asked by: username_0 on 2020-02-17)
  
  I'm trying to use cellranger to `mkfastq` and then `count` and `aggregate` single-cell data. This data was not generated using 10x Genomics RNASeq.
  
  When I run `count`, cellranger fails to auto id the chemistry and crashes out. Is it possible to wrangle the data into the cellranger method or should I look elsewhere. I'd ideally like to use the same method for all my single-cell data but not all of it is 10x.
  
  **Tags:** single-cell, cellranger
  
  > **Comments:**
  > **username_1**: Hi username_0, could you tell us what how you generated the RNAseq data? That might be important. Also what species/problem you are working with?  
  > **username_2**: How do the fastq files that belong to a given sample look like, I mean how are they named? Can you share the `ls` output of a given sample directory?  
  > **username_3**: Perhaps [STARsolo](https://github.com/alexdobin/STAR/blob/2.7.3a/docs/STARsolo.md) is worth looking into.  
  > **username_0**: Hi, It is Smart-Seq2 data that I am hoping to overlap with some 10x data. Regarding the fastq I had to use the mkfastq command. For each sample, I have _R1 _R2 _I1 _I2 files. The naming consists of the sample name, the clone, the lane and the read.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2020-02-17. Score: 1
  
  Possible? Sure. Your biggest problem is that 10x is expecting barcodes from its whitelist. I used to alter the python scripts to accept a 'new' kind of chemistry where the barcodes and umi lengths matched what I had, but I found that my modifications stopped working when the version updated, and I couldn't figure it out, so I started modifying fastqs instead.
  
  > **Comments:**
  > **username_2**: Do you mind sharing the altered code? And how do you modify the fastqs?  
  > **username_4**: My modifications didn't work, and I strongly recommend not changing code like that unless you understand what you are doing.  As to changing the fastqs, you have to understand the format you've got, and what format you want.  I use umi_tools to identify the barcodes and their one-offs, and use that list to make replacements.  
  
  ---
  
  