User: rm16

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rm160
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Posts by rm16

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Convert BLAT to GFF file?
... Does anyone know of a handy script to convert a PSL file from a BLAT alignment to a GFF annotation file? It seems like a PSL has all of the information needed to build a GFF file, but I cannot seem to find a script out there to do the dirty work for me. ...
psl annotation gff alignment blat written 3.2 years ago by rm160
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Comment: C: Remove repetitive sequence of variable length from reads
... I was able to figure it out using extended regular expressions and just running a couple of different scripts to make sure I removed every repetitive instance: sed -E 's/^CCCCAAAA*//g' file.fasta Thanks a lot, everyone. ...
written 3.3 years ago by rm160
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Remove repetitive sequence of variable length from reads
... I am working with a FASTA file in which each read contains a repetitive sequence of variable length at the 5' end. For instance, in the below file: >seq1 CCCCAAAACCCCAAAACCCCGATGATCATGGATC >seq2 CCCCAAAACCCCGATGGCATCATTCA >seq3 CCCCAAAACCCCAAAATATGTTGCTACTAG I woul ...
fasta osx sequencing written 3.3 years ago by rm160 • updated 3.3 years ago by igor8.9k
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Comment: C: awk to clip off telomeres
... That sounds like a good starting place. I think I can adapt this. Thanks a lot! ...
written 3.3 years ago by rm160
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Comment: C: awk to clip off telomeres
... That seems pretty handy. Thank you for the tip. I'll try it out. ...
written 3.3 years ago by rm160
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awk to clip off telomeres
... I want to use the Mac OSX terminal to clip repetitive sequences from the beginning of the each sequence in a fasta file. For example, I would like to make the following file: >seq1 CCCCAAAACCCCATGATCATGGATC >seq2 CCCCAAAACCCCATGGCATCATTCA >seq3 CCCCAAAACCCCATGTTGCTA ...
telomere fasta osx terminal awk written 3.3 years ago by rm160 • updated 3.3 years ago by Farbod3.3k
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Comment: C: Error: segment-based junction search failed with err =-5
... I'm having this same problem now. Any resolution? ...
written 3.5 years ago by rm160
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Comment: C: Tophat error: Bowtie not found on this system
... Sure. I was unclear: I do call it from command line. Read file is located within tophat directory. > tophat genomeIndexPrefix RNAseqReads.fastq ...
written 3.5 years ago by rm160
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Comment: C: Tophat error: Bowtie not found on this system
... Ok, just fixed that. Still getting the error though. ...
written 3.5 years ago by rm160
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Comment: C: Tophat error: Bowtie not found on this system
... I just gave that a shot, but I am still getting the same error. I also ensured that the path to my bowtie2 index directory is in my PATH variable ...
written 3.5 years ago by rm160

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