User: al-ash
al-ash • 110
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- Japan/Okinawa/OIST
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- 4 days, 22 hours ago
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Posts by al-ash
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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 10 weeks ago by
al-ash • 110
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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 11 weeks ago by
al-ash • 110
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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 12 weeks ago by
al-ash • 110
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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 3 months ago by
al-ash • 110
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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 8 months ago by
al-ash • 110
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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 8 months ago by
al-ash • 110
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Comment:
C: SRX from SRR IDs
... Be careful though when converting larger number of accessions. When converting ca 500 Sample accessions to Run accessions, somewhere in the middle of the process, one conversion failed for me with "Can't fetch uids from history because of: Result not ready". ...
written 9 months ago by
al-ash • 110
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... Thanks! https://stackoverflow.com/questions/46626414/how-do-i-generate-all-possible-newick-tree-permutations-for-a-set-of-species-giv/46670077#46670077 is very close - I think I can generate the bifurcating trees by taking this solution and removing the polytomies (which I can do here by e.g. removi ...
written 11 months ago by
al-ash • 110
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... I'd like to generate all existing bifurkating newick trees for a set of N taxa (specifically N=5 for my task but I would prefer a general solution for N).
The tool or code would ideally take as input a set of N strings (e.g. "species1","species2","species3","species4","species5") and generate all p ...
written 11 months ago by
al-ash • 110
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... I think consensus() is not doing what I'm looking for here - to compare a reference tree with a set of some other trees and generate a tree with the same topology as the reference tree but additionally containing conflict/support information accumulated from all the other input trees. ...
written 11 months ago by
al-ash • 110
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Popular Question
7 months ago,
created a question with more than 1,000 views.
For OrthoDB - How to retrieve ortholog groups for only the selected species
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7 months ago,
created a question with more than 1,000 views.
For Entrez Direct E-utilities - using match and xtract to filter by data value
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For How to append strings (from one file) to Fasta headers (in another file)
Teacher
10 months ago,
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For A: How to trim nucleotide sequences to length divisible by 3
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For Entrez Direct E-utilities - using match and xtract to filter by data value
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13 months ago,
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For "Optimal" setting of CPU and max_memory in Trinity
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17 months ago,
created a question with more than 1,000 views.
For How to append strings (from one file) to Fasta headers (in another file)
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For Entrez Direct E-utilities - using match and xtract to filter by data value
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22 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
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23 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
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2.0 years ago,
created a question with more than 1,000 views.
For Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
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For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
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