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Recent Replies
Comment: Problem while uploading DESeq2 library
by
Basti
▴
500
Have your tried to close and reload your R session ? After you can try to reinstall
Comment: Extract sequences from a list of ID
by
Ishak
•
0
thanks
> seqkit grep -r -f id.txt Cucumis_melo.Melonv4.cds.all.fa -o result.fa
it works!
Comment: Different line length in fasta file
by
soumya.oneomics
•
0
I used the same command with my fasta file. But I am still getting the error :
[E::fai_build_core] Different line length in sequence '…
Comment: Problem while uploading DESeq2 library
by
amrsalaheldin50
•
0
I tried to install GenomeInfoDbData by this below command:
```{r}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocM…
Comment: Different line length in fasta file
by
cpad0112
21k
Sorry to say this but this didn't help !
what's the error and what is the command line you are using ?
Comment: Different line length in fasta file
by
soumya.oneomics
•
0
Sorry to say this but this didn't help !
Comment: Problem while uploading DESeq2 library
by
cpad0112
21k
there is no package called ‘GenomeInfoDbData’
try installing that package. Then try loading package ‘GenomeInfoDb’
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…
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