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Old 09-17-2019, 12:00 PM   #13
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,030

Output fasta reads were interleaved (put in one file) since you had paired-end reads to begin with. To separate them into two files you should use the command below.

for i in *.fa; do name=$(basename $(i} .fa); in=${name}.fa out1=${name}_R1.fa out=${name}_R2.fa ; done
You could also do the original conversion by providing "out1=" and "out2=" separate file names during BAM conversion to avoid this step.
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