User: conchoecia

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conchoecia
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Posts by conchoecia

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Answer: A: single line fasta to mult line fasta
... A solution using bioawk and fold. This avoids fold's incorrect behavior to fold long fasta headers. This should work with fasta files that contain multiple sequences. Awk people - I had to use echo twice since printf didn't place the newline in the correct position after the seqname... bioawk ...
written 9 months ago by conchoecia0
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Comment: C: Selecting Random Pairs From Fastq?
... It sounds like you're passing in a file that has interleaved reads. Is that true? In that case, you might get randomly get a forward and reverse pair right next to each other. If so, you need to use seqtk on both the forward and reverse files independently, then interleave them. ...
written 2.4 years ago by conchoecia0
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Answer: A: Downloading And Maintaining A Local, Blast-Able Nr Database
... I made a script that checks if there is a blast job currently running, waits until it is done, deletes the old dbs, then downloads the new ones and moves them into the same directory name. The script outputs everything into a dated log for archival purposes. Anyone have any suggestions for improveme ...
written 2.4 years ago by conchoecia0
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Comment: C: Converting Sam To Bam
... I think this was in reference to the possibility of stderr also directing to the output file when ">" instead of "-o" is used. Found something about it here: https://sourceforge.net/p/bio-bwa/mailman/message/32092344/ Not sure if it's still a problem though! ...
written 2.7 years ago by conchoecia0

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