Extracting reads from fastq files with BBMAP?
Hi I have a file with list of read ids I would like to extract from a pair-end read. This file only contains 1000 reads. When i use bbmap to accomplish this with the following command however, the resulting size of the fastq files are very similar to original and so are
/bbmap/filterbyname.sh in1=${fq1} in2=${fq2} out1=strip2_R1.fq.gz out2=strip2_R2.fq.gz names=names2.txt
This should only have 1000 reads in the new files but its in the millions!
Is there something I'm doing incorrectly? thanks!
• 1,992 views
•
link
updated
by
GenoMax
•
written
by
simplitia •
•
written
by
simplitia •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Reading in input file into a Snakemake pipeline
written by Timotheus •
-
MultiQC output shows that data processing steps are ineffective
written by melissachua90 •
-
Bash loop for bbduk
written by avelarbio46 •
-
BBMap Clumpify error
written by Tania
-
Seeking help with snakemake
written by Ming •
-
How does bbduk calculate it's memory requirements?
written by Lina F
-
Tadpole error with paired end files
written by h.l.wong
-
How to use BBtools repair.sh on multiple files
written by dw845316 •
-
ERROR: while running fastqc on a fastq file
written by Bioinfonext
-
BBTools - Repair.sh bug (?)
written by cacampbell •
What does
names2.txtlook like (show us output ofhead -5 names2.txt)? Remember to remove@or>identifiers from read names innames2.txt. One read name per line in file.Hi, ok here is how the first few lines look like.
You may need to add
substring=t. These should work.