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Recent Replies
Comment: Different line length in fasta file
by
soumya.oneomics
•
0
I used this with a line length of 30000 since the sequence length is large, but the issue still persists.
Comment: Different line length in fasta file
by
Pierre Lindenbaum
146k
https://gatk.broadinstitute.org/hc/en-us/articles/360036483512-NormalizeFasta-Picard-
Answer: blast: error while reading seqid using ncbi database
by
dariober
13k
Re-installing / upgrading blast seems to fix it...:
```
mamba install 'blast>=2.12'
blastn -query reads.fa -db 28S_fungal_sequences …
Comment: Different line length in fasta file
by
soumya.oneomics
•
0
The file was unzipped. I used bgzip to zip before using it for VEP. Thank you for your suggestion.
Answer: Get middle part of a url
by
Joe
20k
Another solution using regex:
$ [[ "ftp.sra.ebi.ac.uk/vol1/sequence/ERZ928/ERZ928990/contig.fa.gz" =~ ([[:alpha:]]{3}[[:digit:]]{6…
Comment: Different line length in fasta file
by
cpad0112
21k
Did you unzip the reference file using bgzip? Try making fasta sequences single lined using seqkit.
`seqkit -w 0 seq input.fa -o output.f…
Comment: How to add taxonomic information to fasta headers
by
Joe
20k
You'll need to post the table in text form for us to be able to help easily.
Comment: Different line length in fasta file
by
soumya.oneomics
•
0
Thank you for your reply.
Seems like I got confused between sequence length and line length. If that's the issue can you help me to recti…
Comment: Script or tool to compare more than two .cls files in R or Python
by
Joe
20k
So to make sure I understand the problem, there is no correspondence between cluster names in each of the files?
As such, you need to iden…
Answer: Different line length in fasta file
by
Pierre Lindenbaum
146k
> I am attaching the length of sequence here
why pasting an image when you can just copy and paste the text ? save the planet.
Your p…
Comment: How do I CATEGORIZE the result of Gene Ontology ?
by
Basti
▴
500
You could have a look at REVIGO : http://revigo.irb.hr
Comment: I am trying to convert a tab file to bed what is the best command to do this?
by
Pierre Lindenbaum
146k
nobody can answer because we don't known what's in your "tab separated file"
but the solution is most likely [awk][1]
version 2.3.6
version 2.3.6