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Recent Replies
Answer: 18S taxonomy assignment SILVA database formatting
by
mbuenner
•
0
My „formatted“ file looks like this:
$ tail SILVA_132_taxonomy_assignment_formatted.fasta
CCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTA…
Answer: 18S taxonomy assignment SILVA database formatting
by
mbuenner
•
0
This is the fasta format of the taxonomy file I would like to change the SILVA database file into:
>Level1;Level2;Level3;Level4;Level5;L…
Comment: Clustalo failing to complete multiple sequence alignments
by
saamhasan55
▴
10
Hi, I know this is an old thread, but I am encountering a similar problem. I am trying to do an msa for the cds sequences of 5 bumblebee sp…
Comment: 18S taxonomy assignment SILVA database formatting
by
antonioggsousa
2.8k
Hi!
Please share first with us an example how the data looks like, the command-line you're running and the problem that you're getting. If…
Answer: Finding sequences in unannotated genomes using reference coordinates
by
Prangan
▴
20
I may have stumbled on a solution for this problem. What I wanted was the SNPs or mutations in the VCF to be incorporated in the reference.…
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
by
prietto
•
0
Thank you. I tried doing a pseudobulk analysis by doing the following:
I have 9 patient ids in a column `Patient` in my metadata, and a co…
Comment: tximport error: vroom
by
ATpoint
77k
It's a problem with the import of the text files (quant.sf) I would say. I cannot really debug the error itself, but can you try
```r
…
Comment: Converting from BED to SAF/GFF
by
ATpoint
77k
It's recommended to make a `Tool` post with usage examples that you can link to.
Answer: Error in checkFullRank(modelMatrix) :
by
ATpoint
77k
Sample is nested with condition and with itself, meaning that each sample is either condition1 or 2, but for a paired design each sample wo…
Comment: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Michael
53k
Software carpentry provides some good [introductory courses in Linux, Git, Python and R][1]. We are using these materials in our local soft…
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴
40
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴
40
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴
40
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
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