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rvalieris / parallel-fastq-dump

parallel fastq-dump wrapper
MIT License
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Forward and reverse identifier /1 and /2 #31

Closed smb20200615 closed 3 years ago

smb20200615 commented 3 years ago

Hello,

Thank you for your wonderful tool. Is there any way I can download the reads with the forward and reverse identifiers? Some downstream applications require these identifiers.

Many thanks!!

rvalieris commented 3 years ago

hello,

please note that parallel-fastq-dump only calls fastq-dump under the hood, so we are limited by the options fastq-dump gives us.

with that said, you can use the option --readids which will add an extra .1 /.2 to the read name

smb20200615 commented 3 years ago

Thank you so much!

smb20200615 commented 3 years ago

Apologies. Is there anyway to switch the .1 and .2 to /1 and /2 when downloading due to issues with bwa in downstream steps? sed -i takes a very long time

rvalieris commented 3 years ago

no, I don't think so.

but what you could do is, map the R1, R2 files with bwa as normal, and then later use picard SamToFastq with the INTERLEAVE option, to will create fastq with /1 and /2