User: liorglic

gravatar for liorglic
liorglic330
Reputation:
330
Status:
Trusted
Location:
Last seen:
3 days, 23 hours ago
Joined:
4 years, 5 months ago
Email:
l*******@mail.tau.ac.il

Posts by liorglic

<prev • 91 results • page 1 of 10 • next >
0
votes
0
answers
983
views
0
answers
Comment: C: Reference-guided assembly from short reads
... Unfortunately no. I do de novo assembly (I use SPAdes) and then scaffold contigs into pseudomolecules using RagTag (successor of RaGOO). Works pretty well for me in most cases. ...
written 3 days ago by liorglic330
0
votes
2
answers
139
views
2
answers
Answer: A: Why does Maker-P output Match-part?
... There is nothing wrong with having match and match_part features in your output gff - these are simply the "evidence" from which MAKER synthesizes gene models. In many cases they are not needed, so to get a gff containing only gene models you can use: `gff3_merge -d -n -g`. ...
written 4 weeks ago by liorglic330
0
votes
2
answers
139
views
2
answers
Comment: C: Why does Maker-P output Match-part?
... Can you please reformat your MAKER output as blockquote or code? it's impossible to read as it is now... ...
written 4 weeks ago by liorglic330
0
votes
1
answer
124
views
1
answers
Comment: C: blastn much slower on longer subject sequences?
... I see. That indeed makes sense, but it's still a bit surprising how bad the effect is. Running ~1600 queries against a genome about 50% larger than the human genome is taking more than two days using 40 CPUs. I still suspect that there's something else going on there. I'll update if I ever find out ...
written 4 weeks ago by liorglic330
0
votes
1
answer
152
views
1
answers
Comment: C: How to remove gaps from sequence alignment?
... Sorry, but your question is unclear. What do you mean by "remove gaps"? why would you want to do that? gaps are part of the alignment result... ...
written 5 weeks ago by liorglic330
0
votes
1
answer
124
views
1
answers
Comment: C: blastn much slower on longer subject sequences?
... I don't think there's a memory issue - the job is limited to 100g RAM, and it's actually using 38g. In general, it seems like the machine is doing fine - lot's of free RAM, no swapping and in fact it looks like most of the time Blast is only using one CPU (?). Regarding your other suggestion - is ...
written 5 weeks ago by liorglic330
0
votes
1
answer
124
views
1
answers
Comment: C: blastn much slower on longer subject sequences?
... That's exactly the point - the search space size is the same, it's only arranged into fewer but larger sequences. Or maybe I didn't understand what you tried to say... ...
written 5 weeks ago by liorglic330
4
votes
1
answer
124
views
1
answer
blastn much slower on longer subject sequences?
... Hello, I encountered a strange issue running blastn. I use the same set of query sequences in two scenarios: 1. Running against a DB of genomic contigs 2. Running against the same contigs, after they have been scaffolded into pseudomolecules The second run is about x100 slower! I should no ...
blast blastn written 5 weeks ago by liorglic330 • updated 5 weeks ago by JC11k
1
vote
0
answers
127
views
0
answers
Selecting samples from a VCF that best represent population variation
... Hello, Suppose I have a VCF file with millions of variants (rows) and thousands of samples (columns). I am looking for a way to select a subset of N samples such that they will maximize, or best represent, the variation in the entire population. There is probably more accurate terminology for that ...
vcf written 6 weeks ago by liorglic330
0
votes
0
answers
136
views
0
answers
Comment: C: Simple genome annotation using transcripts data
... GAWN seems to generate pretty good results and it's quite fast too. There is a fair amount of noise (gene models with very long, unlikely introns and other curiosities), but it can be cleaned using simple cutoffs on alignment stats. I should also note that it's very easy to run GAWN - indeed no nigh ...
written 12 weeks ago by liorglic330

Latest awards to liorglic

Popular Question 3 months ago, created a question with more than 1,000 views. For Genome annotation tools - current status. Machine learning?
Scholar 3 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Supporter 5 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 6 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 9 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Scholar 9 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Popular Question 11 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 12 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 13 months ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id
Scholar 20 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 677 users visited in the last hour