User: v.berriosfarias

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Posts by v.berriosfarias

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Comment: C: bowtie2 using loop on bash with paired-ended reads
... Hello thanks for answering!, yes it seems this worked for me, (the command is running and using my threads), now I'm figuring out how to apply `nohup` over this, this is what happens: nohup for i in *1.fastq.gz ; do dir=/mnt/c/Users/eduar/Desktop/Ubuntu/rawdata_Comau/DEC2017/ ; base=$(ba ...
written 6 days ago by v.berriosfarias0
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Comment: C: bowtie2 using loop on bash with paired-ended reads
... Hello, thanks for your answer :) , yes, the above loop gives me the entire path to my files which corresponds to the "fwd" reads which ends in "_1.fastq-gz" , when you say dry-run the final command, you mean this?: do dir=/mnt/path/DEC2017/ base=$(basename $i _1.fastq.gz) ...
written 6 days ago by v.berriosfarias0
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bowtie2 using loop on bash with paired-ended reads
... Hello, I'm trying to align metagenomic read sequences against a reference set of contigs, the samples are each one splitted in two files (these are paired-ended reads) and I'm trying to make a loop using bowtie2 and at the same time making directly a BAM file without making a SAM file on my director ...
bowtie2 sequence alignment bash written 7 days ago by v.berriosfarias0 • updated 7 days ago by swbarnes28.9k

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