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Rox
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Recent Replies
Comment: Error: Please supply a reference FASTA/GBK/EMBL file with --reference
by
colindaven
4.4k
Type
`echo $ref`
to see if your ref has been saved in an environment
variable. If this is empty it is a problem.
Else reente…
Comment: Retrieve specific fasta sequences from a group of assemblies
by
SushiRoll
▴
100
Great, I'll give it a shot.
Thanks!
Comment: Retrieve specific fasta sequences from a group of assemblies
by
GenoMax
124k
Don't know if there is a ready made tool. You will need to align the gene to your assemblies and then it is a matter of parsing the results…
Answer: NCBI DB and Taxonomy classification
by
GenoMax
124k
Files in `FASTA` directory are just fasta format files for `nt`.
You should download the pre-formatted database files (all `nt` pieces)…
Comment: Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
by
GenoMax
124k
`samtools collate` (to name sort the BAM).
Followed by `samtools fastq` (can be done in one pipe).
`reformat.sh` from BBMap suite. (chec…
Comment: Downloading NT chunks from NCBI and creating a BLAST database
by
GenoMax
124k
That is possible.
Perhaps you are already matching the MD5 sums. If not do that as well in case the download itself is corrupting the fil…
Answer: Coffea arabica var typica and geisha
by
Fabio Marroni
★
2.9k
I am aware of the following *Coffea arabica* assemblies:
1. *C. arabica* var. Geisha from [Phytozome][1] (you may need to register for …
Comment: Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
by
luzglongoria
▴
40
Thank you so much.
I have been reading STAR manual but I donde find any function where you can use an input with an aligned read BAM file.…
Comment: Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
by
luzglongoria
▴
40
Thanks.
I didn't know that we can recover fastq reads from an aligned BAM file.
Is there any specific program for that?
Answer: bedGraph to bigwig
by
colindaven
4.4k
Save yourself the trouble, and go directly from bam to bigwig with deeptools bamcoverage
https://deeptools.readthedocs.io/en/develop/con…
Comment: short read aligners 25-50bp BWA vs BWA-MEM vs Bowtie vs Bowtie2
by
colindaven
4.4k
- Use bwa not bwa mem.
- Not sure about Bowtie vs bowtie2, but keep in mind bowtie1 might be very fast, but does not allow indels (typi…
Comment: Help making ADMIXTURE output digestible
by
dr.fakharunnisa
•
0
Thank you. I will check it out
Comment: What kinase phosphorylates WNK2 at site s49 (and s45) ? And how to deal with cha
by
Michael Dondrup
52k
Here is a counter-example, where we actually make it program itself:
*Human: Given a nucleotide sequence, please explain how to translate …
Comment: expansions and contractions from OrthoFinder
by
mohammadhassanj
▴
230
[https://bioinformatics.stackexchange.com/questions/20435/expansions-and-contractions-from-orthofinder][1]
[1]: https://bioinformatics.…
Comment: Bioconductor drawProteins alternative in Python
by
D3xt3R
•
0
There is a limitation in the project in terms of the programming language to be used.
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