User: al-ash

gravatar for al-ash
al-ash110
Reputation:
110
Status:
Trusted
Location:
Japan/Okinawa/OIST
Last seen:
4 days, 22 hours ago
Joined:
4 years, 5 months ago
Email:
b*********@gmail.com

Posts by al-ash

<prev • 70 results • page 1 of 7 • next >
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Comment: C: Sequence Length Distribution From A Fastq File
... 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-ash110
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Comment: C: Unable to perform tbl2asn for submission of transcriptome to Genbank
... 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-ash110
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Comment: C: Submitting many transcriptomes to TSA - how to automatize?
... 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-ash110
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Submitting many transcriptomes to TSA - how to automatize?
... 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 ...
ncbi submition tsa database transcriptome written 3 months ago by al-ash110
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Comment: C: Multiline Fasta To Single Line Fasta
... ...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-ash110
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Comment: A: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
... "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-ash110
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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-ash110
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Comment: C: Generate all bifurkating newick trees given for N taxa
... 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-ash110
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Generate all possible bifurkating newick trees for N taxa
... 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 ...
generate tree newick written 11 months ago by al-ash110
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Comment: C: Combine node/branch labels from multiple trees into one
... 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-ash110

Latest awards to al-ash

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
Popular Question 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
Popular Question 9 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)
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 11 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
Popular Question 13 months ago, created a question with more than 1,000 views. For "Optimal" setting of CPU and max_memory in Trinity
Popular Question 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)
Popular Question 19 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
Scholar 22 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Scholar 23 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 2.2 years ago, voted at least 25 times.

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