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Popular Question to
bharata1803
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Mensur Dlakic
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morovatunc
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Recent Replies
Answer: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
ATpoint
77k
That's normal and known: https://www.biostars.org/p/91624/
Comment: to annotate BEDPE files
by
Lhl
▴
760
is this what you are looking for?
https://github.com/imgag/ngs-bits/blob/master/doc/tools/BedpeGeneAnnotation.md
Comment: ncbi error report log for validate fastq issue
by
1769mkc
★
1.1k
" you're forced to use it" this is sort of since I have use docker image and then pass the GSM id as list of input first to check if the th…
Comment: ncbi error report log for validate fastq issue
by
ATpoint
77k
I don't think this log is helpful. Can't you just get fastq download links via sra-explorer.info or the tool mentioned by @rob in his answe…
Comment: How the first sequencing template removed in pair end sequencing
by
rfran010
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810
Great! It looks like USER enzyme is used to cleave before the first read sequencing and formamidopyrimidine DNA N-glycosylase is used to cl…
Comment: module and trait correlation for WGCNA
by
andres.firrincieli
3.4k
Hi,
First of all, you should never use DEGs for WGCNA. See @kevinblighe answer: [link][1].
> However, when it comes to module-trait analy…
Comment: identify DEGs across all conditions and per specific conditions
by
luffy
▴
50
@camillab, Please look into Kevin Blighe's response in this [post][1] hope that helps.
[1]: https://www.biostars.org/p/357464/
Answer: Running Rockhopper from a command-line
by
langziv
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50
I managed to resolve the issue by passing absolute paths instead of relative ones.
Comment: Which function is best for pathway analysis?
by
luffy
▴
50
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps.
[1]: ht…
Comment: Bacterial Pangenome Analysis
by
kirankumareripogu
▴
10
Hi @liorglic,
Thank you for your prompt response.
I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
by
YUYANG.OON
•
0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴
360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
by
Chris
▴
180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
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