User: lvogel

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lvogel20
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New User
Location:
Western Europe
Last seen:
6 months ago
Joined:
5 years, 2 months ago
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l*****@gmail.com

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Posts by lvogel

<prev • 41 results • page 1 of 5 • next >
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Comment: C: How to avoid http failure when using rentrez to fetch records from a long list o
... It's working, except for the fact that in some places the file contains ^A characters, followed by what appears to be missing data. I would guess I should delete the whole nt file, and download it again, and see if that works. ...
written 6 months ago by lvogel20
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Comment: C: How to avoid http failure when using rentrez to fetch records from a long list o
... genomax: good idea. I'm downloading it now. I imagine I'll use the descriptions in the fasta headers to search for my species names, because I think the taxids aren't in there. Will have to parse it somehow. If I have trouble I'll post again. Thanks. ...
written 7 months ago by lvogel20
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Comment: C: How to avoid http failure when using rentrez to fetch records from a long list o
... I got blastdbcmd to work for one id at a time, like in the example on the web page: blastdbcmd -db nt -entry all -outfmt "%g %T" | \ awk ' { if ($2 == 9606) { print $1 } } ' | \ blastdbcmd -db nt -entry_batch - -out human_sequences.txt But I have a list of almost 5000 species, and puttin ...
written 7 months ago by lvogel20
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Comment: C: How to avoid http failure when using rentrez to fetch records from a long list o
... Thanks for the information. blastdbcmd looks like an interesting tool. I'll either figure out a way to use it, or just modify my current way with Sys.sleep, etc. Internet connection not so bad--last time I downloaded nt, it only took about a day or two. ;) ...
written 7 months ago by lvogel20
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How to avoid http failure when using rentrez to fetch records from a long list of species names
... I have a list of almost 5000 species of interest, for which I would like to download the sequences from Genbank, to create a custom database. I've been using rentrez, and follwing the tutorial, specifically this example: snail_coi <- entrez_search(db="nuccore", term="COI[Gene] AND Gastropoda[OR ...
ncbi R server error rentrez written 7 months ago by lvogel20
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Comment: C: Metabarcoding amplicon size too long for paired-end sequencing
... Thank you. Those are some really good ideas. I would guess then, that the fact that my sequences are shorter than the full mini-barcode, would be reflected in a higher BLAST e-value? But as long as that's also below the cutoff, then it's still fine. ...
written 8 months ago by lvogel20
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Metabarcoding amplicon size too long for paired-end sequencing
... I am supposed to analyze some metabarcoding reads. However, the forward and reverse reads are unable to be merged due to lack of overlap. I was informed that this is because the sequence was too long, so the forward and reverse sequences couldn't extend far enough to overlap adequately. My question ...
metabarcoding next-gen written 8 months ago by lvogel20 • updated 8 months ago by luckylion0730
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Comment: C: Illumina paired-end reads R1 and R2 mixed together?
... Ah, I took a quick look at it, and they didn't compare VSEARCH, which is what I'm using these days. I've recently found an interesting solution to my original question. I wanted to put all the merged reads in the same orientation, for the next steps of the pipeline, e.g. dereplication, BLAST-ing. So ...
written 10 months ago by lvogel20
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Comment: A: Clustering of metabarcoding reads from many environmental samples
... Hello gb, Actually, I did end up moving on to USEARCH for most of the steps of my metabarcoding pipeline. It worked well and required only minimal scripting knowledge. Recently, however, I've been tasked with even larger datasets, which exceeded the 32-bit memory of the free version of USEARCH. So ...
written 11 months ago by lvogel20
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Comment: C: Dereplication of FASTA file with VSEARCH
... Thanks for the reply. You're right on all counts, as far as I now know, too. Before, I was confused too, and using the wrong version. I'll keep putting all the sequences with headers I want to keep at the top of the fasta, and I'll be able to tell from the uc table if it's not using the names I expe ...
written 16 months ago by lvogel20

Latest awards to lvogel

Popular Question 10 months ago, created a question with more than 1,000 views. For Illumina paired-end reads R1 and R2 mixed together?
Supporter 2.7 years ago, voted at least 25 times.

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