User: al-ash
al-ash • 140
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Posts by al-ash
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... Is edirect supporting retrieval of all annotated features from a record?
Example: I can retrieve all features annotated as "gene" in GenBank record of a mitochondrial genome sequence :
efetch -db nucleotide -id KP026275 -format gene_fasta
However, the retrieved multifasta is missing the feat ...
written 22 days ago by
al-ash • 140
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... No such scripts are part of QIIME 2: these are only in QIIME. ...
written 9 weeks ago by
al-ash • 140
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... +1 for the question
I have very similar question (I want to use existing transcriptome-based phylogenies to constrain several branches in my phylogenetic tree reconstruction based on mitochondrial genome sequences) and I'm failing to find any reference on how to approach this or if it is even a sens ...
written 7 months ago by
al-ash • 140
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Comment:
C: Downloading Data From Mg-Rast
... For downloading raw data (data uploaded by MGRAST user as input data), use following: *file=050.1*
Or you can check for yourself how is the download address constructed by inspecting the "Download" button element and the url to which it leads.
Example:
In the download page "http://www.mg-rast.org/ ...
written 7 months ago by
al-ash • 140
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... Really useful! Only if I want to parse the output (e.g. pipe it into grep) I have to first suppress the stderr message:
*Processed XY reads.
Time: Z seconds.*
Might it be more convenient to have this info also in stdout? ...
written 13 months ago by
al-ash • 140
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... I'm receiving error "[linux64.tbl2asn] File contains unexpected extra data" as well.
This error message is not documented on NCBI. In the source code of tbl2asn (https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c) I can see that this error appears when "FileHasMoreData" is tru ...
written 13 months ago by
al-ash • 140
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... Thanks, that looks handy. But I was actually looking for a method which would mimic as closely as possible the adapter detection on NCBI web - because I actually did adapter trimming as a part of the transcriptome assembly but NCBI is still reporting few adapters here and there: in total 137 suppose ...
written 13 months ago by
al-ash • 140
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... Hi,
Is it possible to automatize submition of a large number of transcriptomes to TSA NCBI database without having to create a new TSA submission for each transcriptome? I have many tens of transcriptomes and submitting them one-by-one would be quite laborious.
Also, is there a way how to simulate t ...
written 13 months ago by
al-ash • 140
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... ...the link is dead and I still get the first line empty after redirecting the output into a file - could you update the answer if there is a more elegant way (not piping through tail) to avoid this? ...
written 18 months ago by
al-ash • 140
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... "ITS (Internal Transcribed Spacer) is part of the non-transcriptional region of the fungal rRNA gene" is a bit misleading (it is like defining DNA as the genetic information carrier of birds - i.e. not incorrect, but...) ...
written 19 months ago by
al-ash • 140
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