Moderator: lieven.sterck

gravatar for lieven.sterck
lieven.sterck3.5k
Reputation:
3,450
Status:
Trusted
Location:
VIB, Ghent, Belgium
Scholar ID:
Google Scholar Page
Last seen:
6 minutes ago
Joined:
2 years, 11 months ago
Email:
l************@gmail.com

Posts by lieven.sterck

<prev • 776 results • page 1 of 78 • next >
0
votes
1
answer
85
views
1
answers
Comment: C: Trimmomatic: LEADING and TRAILING
... unless you have a very specific objective I would go for at least 20 (perhaps even 25-26 nowadays) ...
written 5 days ago by lieven.sterck3.5k
1
vote
1
answer
93
views
1
answers
Answer: A: Is the gene model file and gene annotation file in the Galaxy the same?
... Yes, in theory you can swap those files. You just need to make sure they are both correctly formatted and that they contain the same 'naming' : that eg. gene_id is consistently used to denote the genes (and thus not gene_id in file A and parent_id in file B), or adapt your htseq count cmd accordingl ...
written 6 days ago by lieven.sterck3.5k
0
votes
1
answer
79
views
1
answers
Comment: C: Distinguishing sequencing reads as prokaryotic or eukaryotic without a reference
... can you elaborate a little on what you all have done already? From the top of my head there is not much you can do I think ...
written 6 days ago by lieven.sterck3.5k
1
vote
1
answer
134
views
1
answers
Comment: C: Alignment loop using STAR
... there is a possibility that you're running out of storage space to store the results? Did this not produce any errors then? ...
written 10 days ago by lieven.sterck3.5k
0
votes
1
answer
101
views
1
answers
Answer: A: How can I view and manage the Trinity.fasta by bash
... grep -B1 "TTTGGTGAAATATCGAAA" Trinity.fasta will do the trick , and do `grep -A1 "transcriptID"` to get the reverse, id +sequence Depending on what your goal is, this is likely not the best approach to analyse or manage fasta files (eg. if the pattern you look for is split over two lines you ...
written 11 days ago by lieven.sterck3.5k
0
votes
0
answers
102
views
0
answers
Comment: C: sequencing to identify novel restriction sites
... why not use a protocol suited for smaller fragments? and then do 50bp SE sequencing? ...
written 12 days ago by lieven.sterck3.5k
0
votes
0
answers
102
views
0
answers
Comment: C: sequencing to identify novel restriction sites
... not sure I completely follow. Do you have sequence data already or are you looking for a clever sequencing strategy to ease the post-processing? ...
written 12 days ago by lieven.sterck3.5k
1
vote
1
answer
79
views
1
answers
Comment: C: Blastall vs Blastn
... I see, has been extensively discussed in this forum as well there is a follow-up on that though: from the NCBI blast devs themself (thx @genomax) [https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty1026/5259186][1] [1]: https://academic.oup.com/bioinformatics/ ...
written 12 days ago by lieven.sterck3.5k
1
vote
1
answer
79
views
1
answers
Comment: C: Blastall vs Blastn
... roughly yes. the only (slight) difference is that `-max_target_seqs` is summarized per DB entry ID, while `-num_alginments` is more directly related to the number of HSPs. As such they might, and will, differ if there are multiple HSPs per hit sequence, in that case `-max_target_seqs 1` will report ...
written 12 days ago by lieven.sterck3.5k
2
votes
1
answer
79
views
1
answers
Answer: A: Blastall vs Blastn
... outfmt 6, does not provide descriptions summary, so only the `-num_alignments` is relevant. The old blastall was a bit more lenient towards those two parameters, the blast+ suite is more strict on it and I personally prefer `-max_target_seqs` in tabluar context ...
written 12 days ago by lieven.sterck3.5k

Latest awards to lieven.sterck

Scholar 12 days ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 25 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 25 days ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Scholar 11 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 3 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 3 months ago, created an answer that has been accepted. For A: List of all GO terms
Appreciated 4 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Delete numbers in the tables column
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 4 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Popular Question 5 months ago, created a question with more than 1,000 views. For Assembly with mate-pairs issue
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Scholar 6 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 6 months ago, created an answer that has been accepted. For A: List of all GO terms
Voter 6 months ago, voted more than 100 times.
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 7 months ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 7 months ago, created an answer that has been accepted. For A: List of all GO terms

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1987 users visited in the last hour