Moderator: Sej Modha

gravatar for Sej Modha
Sej Modha4.7k
Reputation:
4,710
Status:
Trusted
Location:
Glasgow, UK
Twitter:
SejModha
Last seen:
16 hours ago
Joined:
6 years, 10 months ago
Email:
s*******@gmail.com

Posts by Sej Modha

<prev • 727 results • page 1 of 73 • next >
0
votes
1
answer
645
views
1
answers
Answer: A: Is it possible to get taxonomy identifiers from diamond output without using --t
... In order to incorporate the taxonomy information into the diamond database, you'd have to use the `prot.accession2taxid` with `nodes.dmp` when you build the diamond database. More info: http://www.diamondsearch.org/index.php?pages/command_line_options/ This can be achieved by using the following ...
written 15 days ago by Sej Modha4.7k
0
votes
1
answer
135
views
1
answers
Comment: C: Smart BLAST or only BLAST?
... That is a new question and completely unrelated to your original question which seems to have been resolved with my initial response. Moreover, I cannot help you with choosing the best hit without any prior knowledge of what you are trying to achieve and what is the question you are trying to answ ...
written 3 months ago by Sej Modha4.7k
1
vote
1
answer
211
views
1
answers
Comment: C: How to make scaffold from contigs
... Most good de novo assembly software contains a scaffold building step as part of the pipeline, e.g. SPAdes. If you want to build scaffolds from existing contigs then you can look into [SSPACE][1] or [Scaffold_builder][2]. [1]: https://www.baseclear.com/services/bioinformatics/basetools/sspace-st ...
written 3 months ago by Sej Modha4.7k
0
votes
1
answer
135
views
1
answers
Answer: C: Smart BLAST or only BLAST?
... SmartBLAST carries out searches against [landmark databases][1] as mentioned on the tool's [home page][2]. If you want to search against those specific databases then you should use SmartBLAST, else use BLAST. PS: https://www.biostars.org/p/357878/ [1]: https://blast.ncbi.nlm.nih.gov/smartbla ...
written 3 months ago by Sej Modha4.7k
0
votes
1
answer
1.8k
views
1
answers
Comment: C: Modifying Fasta file header
... Assuming that your fasta file is called test.fa, you could try `cut -f1-2 -d ' ' test.fa |sed 's/^.*=/>/g'` ...
written 3 months ago by Sej Modha4.7k
0
votes
2
answers
21k
views
2
answers
Comment: C: nr- protein database
... Please do not post new questions in the answer field, it is reserved for answers only. Using the answer field to post a new question is strongly discouraged, please post a new question with relevant details instead. ...
written 3 months ago by Sej Modha4.7k
0
votes
1
answer
186
views
1
answers
Comment: C: Help to run Kaiju through command line interface
... Please use the `ADD COMMENT` box for discussion, the answer field is reserved for answers/solutions. ...
written 3 months ago by Sej Modha4.7k
1
vote
0
answers
117
views
0
answers
Comment: C: Filtering 50 biggest contigs
... You could convert multiline fasta to single line using https://www.biostars.org/p/9262/ and then extract the first 100 lines using `head` which should extract the top 50 contigs for you. ...
written 3 months ago by Sej Modha4.7k
0
votes
1
answer
359
views
1
answers
Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... Thanks for clarifying that, just to check, could you try putting `nanofilt.yaml` at the same directory level as the snakemake file and modify the file path in the script? Re-run the script and see if still get the same error? I am just wondering if snakemake is able to find the env file specified in ...
written 3 months ago by Sej Modha4.7k
0
votes
1
answer
359
views
1
answers
Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... Sorry, you're right, I misunderstood the question. Can you clarify what you mean by 'On my computer, snakemake is already installed' ? Do you mean you have snakemake installed in your base env? ...
written 3 months ago by Sej Modha4.7k

Latest awards to Sej Modha

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 5 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Great Question 6 months ago, created a question with more than 5,000 views. For NCBI Protein GI to Genome Accession
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Scholar 11 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 12 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 14 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 18 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Popular Question 18 months ago, created a question with more than 1,000 views. For NCBI Protein GI to Genome Accession
Appreciated 19 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 20 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 2.0 years ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 2.1 years ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 2.1 years ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 2.2 years ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 2.2 years ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1455 users visited in the last hour