bwa mem problem with Illumina sequence

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5.5 years ago

sevillaro1970 • 0

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 • 2.3k views

ADD COMMENT • link updated 5.5 years ago by finswimmer 16k • written 5.5 years ago by sevillaro1970 • 0

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

ADD REPLY • link 5.5 years ago by h.mon 35k

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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 REPLY • link 5.5 years ago by finswimmer 16k

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

ADD REPLY • link 5.5 years ago by Joe 21k

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