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Recent Replies
Comment: limma+voom flips the sign of the effect from CPM?
by
ATpoint
53k
Cross-posted with code https://support.bioconductor.org/p/9139613/
I bet this is due to improper CPM calculation as OP is using naive per-…
Comment: Unable to download fastq files in parallel / SOS
by
GenoMax
106k
Looks like you have an extra space in your output dir `/scratch/eag88/rnaseqtrial /rawsamples` in your script. Remove the space after `rnas…
Comment: Unable to download fastq files in parallel / SOS
by
Renesh
★
2.0k
First, try to run the command with any accession such as `fastq-dump --split-files SRR8296149` on compute node. If it works, then you have…
Comment: How to extract protein sequences from published paper
by
GenoMax
106k
`22753475` is the PMID. I added the part starting with `grep` onwards to demonstrate that this works. You will need to take that part out t…
Comment: Unable to download fastq files in parallel / SOS
by
eag
•
0
Thanks for the response! I'm following a course so I just followed what they did. Do you have an idea as to why mine wouldn't work?
I trie…
Comment: Filter criteria for variants based on GBS data
by
Renesh
★
2.0k
Here [in this article][1], I have covered some of the filtering criteria for variant filtering from the GBS data. I hope it will be helpful…
Comment: Unable to download fastq files in parallel / SOS
by
Renesh
★
2.0k
SRA-toolkit supports the multithreading option, but it is for single files and not multiple files. I think you mean here batch download ins…
Comment: How to extract protein sequences from published paper
by
Nelo
•
0
First of of thank you so much for replying again
So the number '22753475' is the PMID I guess but what about the last line 'grep ">" | hea…
Comment: Best Omic file compressor?
by
Mensur Dlakic
★
13k
This is not really answering your question, but it may be useful.
Disk storage is relatively cheap compared to time and effort needed to t…
Comment: How to extract protein sequences from published paper
by
Nelo
•
0
Yes some paper mentioned about the accession number but other paper haven't mentioned accession number of protein other than the number of …
Comment: long non coding RNA
by
Hyper_Odin
▴
200
Indeed!
They don't even mention it in the "About" section of the page.
Instead they mention it [here][1].
[1]: https://bioinformatics.…
Comment: limma+voom flips the sign of the effect from CPM?
by
Jautis
▴
330
That's what I thought as well, but it's happening none the less which is why I'm confused. I don't think this is a consequence of small rea…
Comment: Issues installing Pindel from git
by
GenoMax
106k
Install using `conda`. Instructions for installing `conda` ([LINK][1]).
Then do: https://anaconda.org/bioconda/pindel
[1]: https://bio…
Comment: Issues installing Pindel from git
by
Edmond
•
0
Hello, I am having the same issue after 3.9 years. Can any one help me please ?
Comment: How to extract protein sequences from published paper
by
GenoMax
106k
Caveat: This is likely not going to work for most papers. But if you have the right PMID then you could do the following.
$ esearch -d…
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