User: marina.v.yurieva
marina.v.yurieva • 410
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Posts by marina.v.yurieva
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... 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.yurieva • 410
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... 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.yurieva • 410
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... 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 ...
written 20 months ago by
marina.v.yurieva • 410
• updated
20 months ago by
geek_y ♦ 8.6k
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... 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 ...
written 21 months ago by
marina.v.yurieva • 410
• updated
21 months ago by
Amitm • 1.5k
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... Ok, makes sense. Thank you! ...
written 22 months ago by
marina.v.yurieva • 410
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665
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1
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... I have a naive question: what happens if I add "fr-firststrand" option when I run Tophat but don't add it for Cufflinks? ...
written 22 months ago by
marina.v.yurieva • 410
• updated
22 months ago by
Devon Ryan ♦ 81k
0
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1
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850
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1
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... you can convert this python script into perl: https://www.biostars.org/p/1923/
...
written 2.5 years ago by
marina.v.yurieva • 410
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1
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... 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.yurieva • 410
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... You can try some Bioinformatics problems first: http://rosalind.info
...
written 2.5 years ago by
marina.v.yurieva • 410
0
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1
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906
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... 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.yurieva • 410
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