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Recent Replies
Comment: How to download raw sequence data from GEO/SRA
by
cicindel
▴
60
I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ?
by
cpad0112
15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this:
ls *1_1.txt.fa | while read line; do echo ${line%…
Comment: Bioinformatics startup market analysis
by
gtechbio
▴
30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis
by
gtechbio
▴
30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
by
geneticatt
▴
120
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low).
Edit: I may…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴
40
It looks like the following:
system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa"))
GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴
40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first:
blastn.filelist <- s…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★
2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
Answer: question when using topgo
by
seidel
7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Answer: How to get GO terms to specific to perticular biological process
by
geneticatt
▴
120
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
Comment: How to perform multiple alignment using MAFFT?
by
Dunois
▴
620
What does your `system()` command look like now, after having added `--anysymbol`? I am guessing you added `--anysymbol` right before that …
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
Are you using this statement in a loop? If so, please refine your command to error out with the file that produces the error - maybe print …
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