User: al-ash

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al-ash140
Reputation:
140
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Location:
Japan/Okinawa/OIST
Last seen:
1 day, 5 hours ago
Joined:
5 years, 4 months ago
Email:
b*********@gmail.com

Posts by al-ash

<prev • 74 results • page 1 of 8 • next >
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Retrieve all annotated features in a GenBank record
... 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 ...
edirect efetch feature annotations genbank written 22 days ago by al-ash140
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Answer: A: QIIME cannot run python script
... No such scripts are part of QIIME 2: these are only in QIIME. ...
written 9 weeks ago by al-ash140
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Comment: C: Appropriateness of using topology constraints to enforce species tree concordant
... +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-ash140
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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-ash140
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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 13 months ago by al-ash140
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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 13 months ago by al-ash140
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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 13 months ago by al-ash140
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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 13 months ago by al-ash140
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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 18 months ago by al-ash140
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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 19 months ago by al-ash140

Latest awards to al-ash

Popular Question 7 months ago, created a question with more than 1,000 views. For "Optimal" setting of CPU and max_memory in Trinity
Popular Question 9 months ago, created a question with more than 1,000 views. For "Optimal" setting of CPU and max_memory in Trinity
Popular Question 10 months ago, created a question with more than 1,000 views. For Tune criteria for extraction of consensus sequence from bam/sam alignment
Popular Question 18 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 18 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 20 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 20 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 22 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 24 months ago, created a question with more than 1,000 views. For "Optimal" setting of CPU and max_memory in Trinity
Popular Question 2.3 years 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 2.4 years 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 2.7 years ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 3.1 years ago, voted at least 25 times.

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