Moderator: genomax
genomax ♦ 75k
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Posts by genomax
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... If you just need `1:N:0` then you could use `reformat.sh` from [BBMap suite][1].
addcolon=f Append ' 1:' and ' 2:' to read names, if not already present.
[1]: https://sourceforge.net/projects/bbmap/ ...
written 19 minutes ago by
genomax ♦ 75k
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... Hmm. I get the same record for titin if I use the following two URL's. One is for accession and other is for `gi`.
https://www.ncbi.nlm.nih.gov/protein/1212992
https://www.ncbi.nlm.nih.gov/protein/CAA62188.1 ...
written 25 minutes ago by
genomax ♦ 75k
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Comment:
C: Error in PGAP pangenome pipeline?
... So it is likely that there is an error in your input. Have you compared your inputs with the test data to see if you are able to spot what may be wrong? ...
written 2 hours ago by
genomax ♦ 75k
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... Using Entrezdirect (linked above) you can get the `gi` where possible:
$ esearch -db protein -query "CAA62188" | efetch -format gi
1212992
$ esearch -db protein -query "AAD36848" | efetch -format gi
4982364
As for the numbers not matching that is interesting (as above). Since autho ...
written 2 hours ago by
genomax ♦ 75k
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... Did you make the bowtie v.1 indexes yourself or downloaded them from somewhere? Are they known to work? ...
written 3 hours ago by
genomax ♦ 75k
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... Which pipeline are you referring to? Perhaps it could be modified to use accession numbers? ...
written 3 hours ago by
genomax ♦ 75k
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Comment:
C: Qiime2 Demux Error
... You need to actually run Qiime2 analysis to get the `.qza` files.
As for your second question it may. Qiime2 evolved over years to use different inputs. Take a look at the [input section in the tutorial][2] for more.
[1]: https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Qiime2.html ...
written 3 hours ago by
genomax ♦ 75k
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... Please do not use `gi` numbers they have been deprecated for end-user use by NCBI for almost 2 years now. Stay with accession numbers where you can.
That said [EntrezDirect][1] should be able to get this information. It seems to be not behaving at the moment though.
[1]: http://bit.ly/entrez-di ...
written 4 hours ago by
genomax ♦ 75k
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... Yes. It is a new book that is included as a part of your subscription to Biostars Handbook. ...
written 4 hours ago by
genomax ♦ 75k
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... https://www.biostars.org/u/30494/ : Would this method work for 10^7 gi numbers? Those are a lot to deal with irrespective of the method. ...
written 17 hours ago by
genomax ♦ 75k
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For C: is it code is python + bash .....and what is this AssignGenes.py ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: is it code is python + bash .....and what is this AssignGenes.py ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For A: How to get nuclear and mitochondrial gene sequences ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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For C: How do I download mm10 major release genomic fasta and gtf file?
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For A: Concatenating fastq.gz files across lanes
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For C: is it code is python + bash .....and what is this AssignGenes.py ?
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For C: is it code is python + bash .....and what is this AssignGenes.py ?
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