hi everybody, I am new in this field. I have a qseq file output of illumina GA.
Before continuing the analysis (mapping against the genome) I would appreciate some help. I have more than 40 millions of reads, but 11 millions have the filtering bit (last column of the file, the column 11th) with 0 (no passing filtering), so my question is if I have to remove those reads before mapping or filtering it during mapping with bowtie that can filter those reads.
Thanks.
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