User: al-ash
al-ash • 150
- Reputation:
- 150
- Status:
- Trusted
- Location:
- Japan/Okinawa/OIST
- Last seen:
- 2 days ago
- Joined:
- 5 years, 8 months ago
- Email:
- b*********@gmail.com
Posts by al-ash
<prev
• 74 results •
page 1 of 8 •
next >
1
vote
0
answers
170
views
0
answers
... 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 4 months ago by
al-ash • 150
0
votes
1
answer
1.9k
views
1
answers
... No such scripts are part of QIIME 2: these are only in QIIME. ...
written 6 months ago by
al-ash • 150
0
votes
0
answers
739
views
0
answers
... +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 11 months ago by
al-ash • 150
0
votes
2
answers
11k
views
2
answers
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 11 months ago by
al-ash • 150
0
votes
8
answers
51k
views
8
answers
... 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 16 months ago by
al-ash • 150
0
votes
0
answers
1.1k
views
0
answers
... 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 17 months ago by
al-ash • 150
0
votes
0
answers
388
views
0
answers
... 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 17 months ago by
al-ash • 150
1
vote
0
answers
388
views
0
answers
... 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 17 months ago by
al-ash • 150
0
votes
10
answers
59k
views
10
answers
... ...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 22 months ago by
al-ash • 150
0
votes
0
answers
3.0k
views
0
answers
... "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 23 months ago by
al-ash • 150
Latest awards to al-ash
Great Question
6 weeks ago,
created a question with more than 5,000 views.
For Make matrix of protein pairwise identities/similarities from multiple protein sequences
Great Question
8 weeks ago,
created a question with more than 5,000 views.
For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Make matrix of protein pairwise identities/similarities from multiple protein sequences
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Make matrix of protein pairwise identities/similarities from multiple protein sequences
Popular Question
11 months ago,
created a question with more than 1,000 views.
For "Optimal" setting of CPU and max_memory in Trinity
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
13 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
21 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
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
23 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
2.0 years ago,
created an answer with at least 3 up-votes.
For A: How to trim nucleotide sequences to length divisible by 3
Popular Question
2.1 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
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For "Optimal" setting of CPU and max_memory in Trinity
Popular Question
2.7 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
2.7 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
3.0 years ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Popular Question
3.2 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
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter
3.4 years ago,
voted at least 25 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1486 users visited in the last hour