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Old 12-08-2016, 05:05 PM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Quote:
Originally Posted by zhanghao View Post
another question is:

I have 3 pairs of pair-end fastq data sets, how to set them as input? In hisat2, I can use "-1 read_A_1.fq,reads_B_1.fq,reads_C_1.fq -2 read_A_2.fq,reads_B_2.fq,reads_C_2.fq", in bbmap, it seems just in1 and in2 are supported.
Hi! Sorry, somehow I missed your post. BBMap only supports a single library per run; if you have different libraries with different insert sizes, I recommend NOT combining them, since BBMap's alignment score is affected by how close the insert size of a pair is to the average.

But you can use bbwrap.sh, as suggested by antoinefelden.

As for the failures of "bs.sh" - this is strange. I'll look into it tomorrow. Maybe it's a difference between Samtools v0.x versus Samtools 1.x - some of the behavior was altered; and bs.sh was designed for Samtools 0.1.19.
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