New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FASTQ input format needs to support index sequences #1697

Closed
fnothaft opened this Issue Aug 29, 2017 · 5 comments

Comments

Projects
None yet
2 participants
@fnothaft
Copy link
Member

fnothaft commented Aug 29, 2017

Related to #1585. There's another Illumina FASTQ spec out there that puts the index sequences in the read name. From the "home of the FASTQ spec":

@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

I've also seen something like this for paired sequences:

@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG+ATCACG

This is close to but slightly different from the variant in #1585.

@heuermh

This comment has been minimized.

Copy link
Member

heuermh commented Aug 29, 2017

The "spec" as it were is this paper, what you are describing is more stuff-whatever-the-hell-in-the-description-line, which has been an ongoing problem with FASTA format for like 20 years. 😄

@heuermh

This comment has been minimized.

Copy link
Member

heuermh commented Jun 26, 2018

for like 20 years.

Shit, I just realized I've been doing this for more than 20 years already. And FASTA the tool was published in 1985.

@heuermh

This comment has been minimized.

Copy link
Member

heuermh commented Jun 26, 2018

From gitter, a pair of reads with index sequences:

@HISEQ_HU01:89:H7YRLADXX:1:1101:1116:2123 1:N:0:ATCACG
@HISEQ_HU01:89:H7YRLADXX:1:1101:1116:2123 2:N:0:ATCACG
@heuermh

This comment has been minimized.

Copy link
Member

heuermh commented Jun 28, 2018

Fixed by #2004

@heuermh heuermh closed this Jun 28, 2018

@heuermh heuermh added this to the 0.24.1 milestone Jun 28, 2018

@heuermh

This comment has been minimized.

Copy link
Member

heuermh commented Jul 5, 2018

Reopening per e7cbfcd#r29602988

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment