User: computationalvarun

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Posts by computationalvarun

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Job failures at http://usegalaxy.org 2016-12-12
... dear galaxy team i am working on human single end illumina data i want to imprve the mapping alignment as i am getting 55 % only. i am trying to use clip, trim, trim galore but nthng works.. failed jobs. what should i do...please help tia ...
trimmomatic clip trim tophat trim galore written 12 months ago by computationalvarun20 • updated 12 months ago by Jennifer Hillman Jackson23k
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Comment: C: What to do when alignment rate is low even though the genomic data and RNA-seq d
... hi mayank ..could you improve your mapping perentage. ia m also stuck with the sam e. have tried trimming , clipping etc. but n o lucky yet. ...
written 12 months ago by computationalvarun20
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unable to run tophat on trim galore processed reads
... dear sir i have run tophat on reads trimmed by trim galore with reference to hg19. i am getting red colored error. i have tried it many times. i ahve downloaded the genome from ucsc browser as well. i ghave trimmed the reads with trim galore using 5' AGTCCGACGATC nad 3' ATCTCGTATGCC adapters. pleas ...
trimgalore mapping tophat written 12 months ago by computationalvarun20 • updated 12 months ago by nishashoolini.phd0
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Comment: C: gff to gtf conversion
... thank you jen. i will try the same. ...
written 12 months ago by computationalvarun20
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Comment: C: gff to gtf conversion
... thank you devon. i will try again. in tophat using full parameter list i am choosing use gene annotation model. in that it is not showing grch37 although it is showing it in my history of galaxy account. i hav echosen hg19 as reference genome. how to go about it. thanks ...
written 12 months ago by computationalvarun20
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gff to gtf conversion
... hi i have uploaded gff format GRCh37.p13 in glaxy. however i am unable to see it on doing any analysis like for tophat and cufflink. how can i do it. how do i convert it to gtf for using it as a reference genome for tophat. it is a human genome. thanks a lot. regards ...
rna-seq gtf tophat gff written 12 months ago by computationalvarun20 • updated 7 months ago by Guy Reeves1.0k

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