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Recent Replies
Comment: Query regarding extraction of GTF file
by
seidel
9.8k
Have you tried reading the gtf file with [python and gtf_parse][1]? That should give you a data structure with columns for each of the attr…
Answer: ReactomePA enrichPathway function
by
landenshanie
•
0
Check that the universe you input are ***characters*** and not ***numerics***. The entrez ID are numbers so R recognizes them as numerics, …
Comment: DESeq or FPKM
by
seidel
9.8k
What @ialbert said. But even before that: "evaluate the gene expression of a large dataset..." doesn't have a question in it. What are the …
Comment: TDF to bed graph -- IGV on command line
by
a_bis
▴
30
(I also tried running ./igvtools [command] [input] [output] and it gave me the same error message!)
Comment: TDF to bed graph -- IGV on command line
by
a_bis
▴
30
Hi GenoMax, many thanks for the reply. I'm not in the install directory (I'm not sure where it is -- is it most likely the Applications dir…
Answer: How can I get sample sequence from bam file?
by
GenoMax
123k
Follow this tutorial to get a consensus: https://www.biostars.org/p/367960/
Comment: Create a nested dictionary from a text file
by
Mensur Dlakic
★
21k
Not sure what you are asking here. Is it about the parsing script I recommended? If so, it is easy enough for you to run it and find out, a…
Comment: TDF to bed graph -- IGV on command line
by
GenoMax
123k
This looks like the classic `$PATH` problem. If you are in the IGV install directory you may simply need to do `./igvtools` and/or add the …
Comment: Missing phage genome in SRA metagenomic data
by
GenoMax
123k
Consider emailing SRA support and the submitter's with relevant information. This may get fixed eventually.
Comment: Missing phage genome in SRA metagenomic data
by
mendonca_thiago22
▴
20
It seems like a database error indeed
Comment: Missing phage genome in SRA metagenomic data
by
mendonca_thiago22
▴
20
Just tried that, had positive hits but with percentage identity below 100. No hits when using as query the phage gene that I'm investigatin…
Comment: Using Salmon to map RNA-Seq and Ribosome Profiling reads in Yeast and downstream
by
kyusikkim
▴
20
That's a good point. I think making the custom annotation, mapping to the genome using STAR, and then using HTSeq for both the RNA-seq and …
Comment: scRNA-seq from SRA
by
GenoMax
123k
You may have only index because the samples may have been independently submitted under separate SRR#.
Comment: scRNA-seq from SRA
by
GenoMax
123k
R1 = UMI+ Cell barcodes<br>
R2 = Actual cDNA read
So R2 will always be longer than R1.
You may have only index because the samples may h…
Comment: ImportError: cannot import name 'transpose' from partially initialized module 't
by
Michael Dondrup
52k
Sorry, I can't because I don't have or know the script or any reproducible data to make that case. I think the problem is in general that t…
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