Differing sequence lengths

[Nancy Sheridan]

Hello,

I'm using Stacks 2.3e and demultiplexed my ddRAD SE raw reads without issue. Before proceeding with ustacks, I used Bowtie2 as a way to filter my anthozoan reads from its known symbiont by mapping to that symbiont's genome. So the resulting unaligned reads (presumably anthozoan) are what I want to use for downstream analysis. When using those .fq.gz files for ustacks, I found that some individuals have differing lengths and I'm getting the following error message with ustacks:

Error: different sequence lengths detected, this will interfere with Stacks algorithms, trim reads to uniform length (override this check with --force-diff-len).

Should I run these .fq.gz files through process_radtags again or is there another way to trim the reads? I did try to run ustacks with the --force-dff-len option, but it didn't work; my test of 4 individuals only had output for 1 of those 4.

Thanks for any/all help.

Nancy

[Daniel Dols]

Hi! You can always truncate your reads' lenghts by using the -t flag in process_radtags. 

This way process_radtags will discard those reads below the specified length and truncate ones above.

Cheers!

 

El dv., 7 de febr. 2020, 20:41, Nancy Sheridan <nshe...@mail.usf.edu> va escriure:

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Nancy Sheridan]

Thank you! This worked.

On Friday, February 7, 2020 at 2:56:59 PM UTC-5, Dan wrote:

Hi! You can always truncate your reads' lenghts by using the -t flag in process_radtags. 

This way process_radtags will discard those reads below the specified length and truncate ones above.

Cheers!

El dv., 7 de febr. 2020, 20:41, Nancy Sheridan <nshe...@mail.usf.edu> va escriure:

Hello,

I'm using Stacks 2.3e and demultiplexed my ddRAD SE raw reads without issue. Before proceeding with ustacks, I used Bowtie2 as a way to filter my anthozoan reads from its known symbiont by mapping to that symbiont's genome. So the resulting unaligned reads (presumably anthozoan) are what I want to use for downstream analysis. When using those .fq.gz files for ustacks, I found that some individuals have differing lengths and I'm getting the following error message with ustacks:

Error: different sequence lengths detected, this will interfere with Stacks algorithms, trim reads to uniform length (override this check with --force-diff-len).

Should I run these .fq.gz files through process_radtags again or is there another way to trim the reads? I did try to run ustacks with the --force-dff-len option, but it didn't work; my test of 4 individuals only had output for 1 of those 4.

Thanks for any/all help.

Nancy

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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