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Old 12-08-2016, 03:26 PM   #3
antoinefelden
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Location: Wellington, NZ

Join Date: Dec 2016
Posts: 4
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I have the same problem, looking at the SAMTools manual, I have the feeling there is a problem on the output option of this command:

Quote:
Originally Posted by zhanghao View Post
samtools view -bSh1 cyp51c_bb.sam | samtools sort -m 13G -@ 3 - cyp51c_bb_sorted
samtools index cyp51c_bb_sorted.bam
bs.sh (END)
Could it be missing a "-o" before the filename? Have a look at the SAMTools page here : http://www.htslib.org/doc/samtools.html

Then it would be
Code:
samtools view -bSh1 cyp51c_bb.sam | samtools sort -m 13G -@ 3 -o cyp51c_bb_sorted
samtools index cyp51c_bb_sorted.bam
bs.sh
However, I could not find any trace of this bs.sh file (I could only find it in my output), so I'm a bit puzzled about how to fix this.

Also, about your second question, you have to use bbwrap instead of bbmap, that will do the job I think

Code:
bbwrap.sh in1=read_A_1.fq,reads_B_1.fq,reads_C_1.fq in2=read_A_2.fq,reads_B_2.fq,reads_C_2.fq ref=genome.fasta nodisk out=cyp51c_bb.sam bamscript=bs.sh; sh bs.sh
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