User: marina.v.yurieva

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Farmington, CT
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Posts by marina.v.yurieva

<prev • 90 results • page 1 of 9 • next >
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Comment: A: Gene names in Ballgown differential expression analysis
... I'm having this problem too and fixed the annotation the same way as Albert but still trying to figure out how to do everything at the gene level. ...
written 19 months ago by marina.v.yurieva410
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Comment: C: Counts from cuffdiff VS featurecounts
... Yes, I saw it but can it be so different that one transcript has 0 counts in featurecounts and several thousands in cuffdiff counts? And then what to use cuffdiff counts for? Clearly you cannot input them in edgeR or DESeq right? ...
written 20 months ago by marina.v.yurieva410
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Counts from cuffdiff VS featurecounts
... I tried to get the information about read counts from the BAM files using both cuffdiff (isoforms.count_tracking file) and featurecounts using the same BAM files and gtf file and for several transcripts they show completely different results. Is it normal or something is going wrong? I tried to run ...
cufflinks counts rna-seq written 20 months ago by marina.v.yurieva410 • updated 20 months ago by geek_y8.6k
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InterPro Scan error with nucleotide sequences
... I'm running InterPro Scan on my nucleotide sequences and it gives this error: Error output from binary: bin/blast/ncbi-blast-2.3.0+/rpsbproc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bin/blast/ncbi-blast-2.3.0+/rpsbproc) It works fine with the protein sequenc ...
sequence domain database written 21 months ago by marina.v.yurieva410 • updated 21 months ago by Amitm1.5k
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Comment: C: Tophat/Cufflinks for stranded RNA-seq data
... Ok, makes sense. Thank you! ...
written 22 months ago by marina.v.yurieva410
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Tophat/Cufflinks for stranded RNA-seq data
... I have a naive question: what happens if I add "fr-firststrand" option when I run Tophat but don't add it for Cufflinks? ...
rna-seq written 22 months ago by marina.v.yurieva410 • updated 22 months ago by Devon Ryan81k
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Answer: A: Retriving the base and its quality from fastq file
... you can convert this python script into perl: https://www.biostars.org/p/1923/ ...
written 2.5 years ago by marina.v.yurieva410
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Answer: A: Best way to generate rarefaction curves from 16S/18S data-reclustering?
... You are right, QIIME scripts for rarefaction plots use #1 http://qiime.org/scripts/multiple_rarefactions.html #2 would be a way to go except it takes much longer and you'll have to do it yourself (there are no scripts for it) but go ahead if you have time. ...
written 2.5 years ago by marina.v.yurieva410
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Comment: C: Bioinformatics project for a beginner
... You can try some Bioinformatics problems first: http://rosalind.info ...
written 2.5 years ago by marina.v.yurieva410
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Answer: A: Simulating single end reads with dwgsim
... Looks like single end is default: -S 0  https://github.com/nh13/DWGSIM/wiki/Simulating-Reads-with-DWGSIM ...
written 2.5 years ago by marina.v.yurieva410

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