User: liorglic

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liorglic340
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Posts by liorglic

<prev • 96 results • page 1 of 10 • next >
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Comment: C: Minia assembler _ header information
... Did you figure it out? I wanted to ask the same question... ...
written 6 weeks ago by liorglic340
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Answer: A: Is ENA API down?
... Just updating that indeed there was a problem with the server, which is now fixed. Works for me now. ...
written 6 weeks ago by liorglic340
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Is ENA API down?
... I'm trying to fetch some data from the ENA API, but keep getting error messages. This has been like that for a few days. Anyone knows if the service is down, or is it me doing something wrong? For example, I try the URL `https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRR1945842&res ...
ena written 6 weeks ago by liorglic340
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Using Aspera to download from GSA (BIG)
... Hello, I need to download WGS data from the [GSA][1] server. I usually download from ENA, using Aspera to increase download speed (specifically, using [ena-fast-download][2]). Anybody knows if/how I can use Aspera to download from GSA? I found [this document][3] which explains how to **upload** t ...
download aspera gsa written 7 weeks ago by liorglic340
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Answer: A: Alignng RNAseq data for gene prediction
... I think you can map everything at once. If you are worried that you might loose isoform information - you can also do it separately for each tissue and merge only at the end. I had pretty good experience with [GAWN][1] for that type of analysis - check it out. [1]: https://github.com/enormandeau ...
written 3 months ago by liorglic340
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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 4 months ago by liorglic340
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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 5 months ago by liorglic340
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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 5 months ago by liorglic340
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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 5 months ago by liorglic340
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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 months ago by liorglic340

Latest awards to liorglic

Scholar 6 weeks ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 3 months ago, created a question with more than 1,000 views. For Merging multiple sets of transcripts (generated by Trinity)
Popular Question 4 months ago, created a question with more than 1,000 views. For Genome annotation tools - current status. Machine learning?
Popular Question 7 months ago, created a question with more than 1,000 views. For Genome annotation tools - current status. Machine learning?
Scholar 7 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Supporter 9 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 11 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 13 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Scholar 14 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Popular Question 16 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 17 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 17 months ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id
Scholar 2.0 years ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

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