Question: bwa mem problem with Illumina sequence
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gravatar for sevillaro1970
17 months ago by
sevillaro19700 wrote:

hi I have a problem with my bwa mem, I have to aligner a sample to run in Illumina. people told me that I have to add this line @RG\tID:'"$i"'\tLB:'"$i"'\tSM:'"$i"'\tPL:ILLUMINA' , where de symbol $I is my sample but the program doest work and always send me a message

Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]
$ bwa mem -t 3 ~/Homo_sapiens.GRCh37.dna.primary_assembly.fa -R '@RG\tID:'"$1545906_17296"'\tLB:'"$1545906_17296"'\tSM:'"$1545906_17296"'\tPL:ILLUMINA' / ~/17296_R1trim_cut.fastq  ~/17296_R2trim_cut.fastq > ~bwa1545906_17296.sam

anybody can help me

next-gen • 518 views
ADD COMMENTlink modified 17 months ago by finswimmer13k • written 17 months ago by sevillaro19700

Please edit your post to format the code and error message. Use the code button (the 101010 button).

ADD REPLYlink written 17 months ago by h.mon29k

Hello,

take care of the order of your arguments. At first there must be the options (-tand -R), than the reference sequence and at the end the fastq files.

fin swimmer

ADD REPLYlink written 17 months ago by finswimmer13k

What are you trying to do (with that string in particular?), and what error is it giving you?

ADD REPLYlink written 17 months ago by Joe16k
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