Question: how to exclude sequence from sam file?
gravatar for Medhat
5.3 years ago by
Medhat8.6k wrote:

The issue that I have Illumina mate pairs sequence, I filtered them using sekwer  it results in two fastq files forward and revers.

there   is some sequences that was removed from one of the files "did not pass the filtering process"

when I use bowtie2 it gives this error:

Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of 'int'
bowtie2-align died with signal 6 (ABRT)


Is there any script or software to exclude those sequences from the two files or I need to write my own?

ADD COMMENTlink modified 3.1 years ago • written 5.3 years ago by Medhat8.6k
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

There's a convenient tool in BBtools for this. Otherwise, see A: How To Sort Two Mate Pair (Fastq) Files So That The Order Of The Identifiers Is .

ADD COMMENTlink written 5.3 years ago by Devon Ryan93k

I tried BBtools worked fine and have a very good and helpful options thanks a lot 

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Medhat8.6k
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