Questions tagged [bash]

The tag has no usage guidance, but it has a tag wiki.

3 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
3
votes
0answers
133 views

Error given while trying to index a BAM file with Samtools Index - NO COOR?

I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to ...
0
votes
0answers
22 views

Retrieve sequence data from just one geneID and not the identical sequences with blastdbcmd

I'm trying to retrieve the sequence from the gene id in NCBI's nr. If I try doing blastdbcmd -db nr -entry 1008808716 I get with this result: ...
0
votes
1answer
27 views

How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...