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Recent Replies
Comment: Error in fetching the Refseq using Taxonomic ID
by
Nelo
•
0
opps
My mistake
not very much familiar with this, but will keep in mind next time
Actually i got the same isses like this:
" ERROR in fil…
Answer: Pseudogenes in the human genome annotation
by
Luis Nassar
▴
540
Hello,
You can also use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to extract the pseudogenes from our default gene tra…
Comment: Rsubread FeatureCounts return 0.0% assigned
by
Bonita
▴
10
OK I will have a look at that. Subread does not index the BAM files so I'll have to do that first.
Comment: Rsubread FeatureCounts return 0.0% assigned
by
GenoMax
107k
I see it now. Thanks for pointing that out.
I suggest that you fire up a genome browser (IGV works well) and examine your alignment files…
Comment: Rsubread FeatureCounts return 0.0% assigned
by
Bonita
▴
10
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/
If you follow the above link there is a button on the right hand side that says Do…
Comment: Rsubread FeatureCounts return 0.0% assigned
by
GenoMax
107k
Can you post a link for the file? I only see GFF files on the [genome page][1].
[1]: https://www.ncbi.nlm.nih.gov/genome/?term=txid1009…
Comment: Output file from samtools index is empty
by
cpad0112
17k
can you please run `samtools quickcheck` on your bam file? Here is the manual: https://www.htslib.org/doc/samtools-quickcheck.html and if y…
Comment: Rsubread FeatureCounts return 0.0% assigned
by
Bonita
▴
10
Yes the file is .gtf. Both were available through the download link on the side but Rsubread seems set up for the GTF files, even though it…
Comment: Pseudogenes in the human genome annotation
by
linmarnor
•
0
Thank you for the link!
Do you mind to explain the query a bit more? I do not understand how modifying only the attributes, one gets the l…
Comment: Rsubread FeatureCounts return 0.0% assigned
by
GenoMax
107k
Are you sure you got GTF format files? NCBI generally makes GFF format files for annotation.
Comment: Count number of unique alignments to each chromosome from sam file
by
GenoMax
107k
Take a look at `pileup.sh` from [**BBMap suite**][1]. Use `secondary=f` flag to exclude those alignments.
[1]: https://sourceforge.net/…
Comment: how to convert output of bash script to .csv ?
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cpad0112
17k
shouldn't it be `paste -d "," - - - -` ?
Comment: how to convert output of bash script to .csv ?
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cpad0112
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Please post the expected output.
Comment: Restrict blastp search to set of specific species
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GenoMax
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> Is it possible using the web browser version of blast to efficiently
> limit my search without manually entering each of the taxid I wish…
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I quickly wrote http://lindenb.github.io/jvarkit/BamToHaplotypes.html
the input is an indexed VCF (only diallelic SNP are considered) an…
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