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Comment: FreeBayes vs GATK's HaplotypeCaller
by
cicindel
▴
70
I think file size, based on the following sentence.
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
I don't see `GENE` being assigned values, so I'm guessing there is yet another loop wrapping the code above. Write the value of `GENE` to s…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴
70
Interesting, I did not think about it like that. Tablet has several colour schemes in the 2nd tab (I think) to visualize different features…
Answer: Trimmomatic-0.36 not finding adapter directory
by
Istvan Albert
87k
Download the adapters and use them by passing the actual path, existing paths to the adapter file.
See the adapters here
https://git…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
Istvan Albert
87k
in all fairness, Tablet did not exist when this thread was started. It is quite impressive that Tablet is still operational though, I gave …
Comment: Trimmomatic-0.36 not finding adapter directory
by
GenoMax
99k
Order of `fastq` file names is important for `trimmomatic`. Make sure that is correct.<br>
Does `ls -lh /usr/local/bin/Trimmomatic-0.36/` …
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴
70
No love for [Tablet][1]? I'm quite surprised to not see it mentioned here. Of course, IGV is the classic, and Tablet is a bit simpler than …
Comment: How to download raw sequence data from GEO/SRA
by
cicindel
▴
70
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…
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