Moderator: genomax

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genomax75k
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Posts by genomax

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Comment: C: Barcode Fastq Header - Adding Characters
... 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 genomax75k
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Comment: C: Convert huge list of accession numbers to GI numbers
... 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 genomax75k
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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 genomax75k
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Comment: C: Convert huge list of accession numbers to GI numbers
... 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 genomax75k
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Comment: C: Could not locate bowtie index (miRDeep2 analysis)
... Did you make the bowtie v.1 indexes yourself or downloaded them from somewhere? Are they known to work? ...
written 3 hours ago by genomax75k
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Comment: C: Convert huge list of accession numbers to GI numbers
... Which pipeline are you referring to? Perhaps it could be modified to use accession numbers? ...
written 3 hours ago by genomax75k
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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 genomax75k
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Comment: C: Convert huge list of accession numbers to GI numbers
... 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 genomax75k
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Yes. It is a new book that is included as a part of your subscription to Biostars Handbook. ...
written 4 hours ago by genomax75k
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Comment: C: Mapping many GI numbers returned from ESearch to Accessions from nr.gz (non-redu
... 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 genomax75k

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Teacher 7 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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Scholar 12 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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Scholar 17 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
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