User: lelle

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lelle780
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Berlin
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Posts by lelle

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Downloading full BlastKOALA results?
... the way I would do this is by writing a bash script that calls wget with each protein ID. Something like this: while read PROT; do echo "$PROT" wget "https://www.kegg.jp/kegg-bin/blastkoala_result_gene_list?id=39732d974cf46cbc344f96d5d7e81bb69c18dcea&passwd=XXxxXX&type=blast ...
written 3 months ago by lelle780
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Answer: A: Downloading full BlastKOALA results?
... I had quick look at this on my blastKOALA Result. When I click on one of my queries I get a detailed list of matches. The list has an URL like this: https://www.kegg.jp/kegg-bin/blastkoala_result_gene_list?id=39732d974cf46cbc344f96d5d7e81bb69c18dcea&passwd=x3XXyz&type=blastkoala&code=u ...
written 3 months ago by lelle780
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Comment: C: Dereplication of FASTA file with VSEARCH
... The --relabel_keep is working fine for my in version 2.4.3. "--relabel keep" should rename all you sequences to keep1, keep2, keep3 and so on Anyway, I think I completely misinterpreted your original question. I don't know why I was thinking you were using hashes. Sorry. If you just run "vsearch -- ...
written 16 months ago by lelle780
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Answer: A: Dereplication of FASTA file with VSEARCH
... You can use the --uc *filename* option to get a detailed table which tells you which sequences are represented by which sequence. Of course to map that back with your blast results will be some work... EDIT: removed the suggestion to use --relabel_keep, because it actually has nothing to do with th ...
written 17 months ago by lelle780
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Comment: C: FastQC's report -- 'Per base sequence content' heading odd wave
... I think you need to find out what causes the bias. If it is Nextera bias, I agree with James, that you should not trim them. If it is something else, like a primer sequence, it might be advisable to remove it... ...
written 17 months ago by lelle780
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Comment: C: FastQC's report -- 'Per base sequence content' heading odd wave
... I don't know... The second and third graph look a bit too strongly biased to be "just" nextera bias, in my opinion. Hard to say without further information on the library... ...
written 17 months ago by lelle780
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Comment: C: demultiplex a dataset when you have barcodes as a separate fastq
... Yes, with the -br option. I am not sure if it works when you have to barcode read files. ...
written 17 months ago by lelle780
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Answer: A: demultiplex a dataset when you have barcodes as a separate fastq
... I agree with Devon Ryan that it is probably easiest to get the data in the format you want from your sequencing provider, If that is not possible, you can use [Flexbar][1] which supports separate barcode reads. [1]: https://github.com/seqan/flexbar ...
written 17 months ago by lelle780
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Comment: C: Clustering PacBio CCS reads
... I don't think the -nonredundant option would address my problem. I want the sequences clustered by full length similarity. Unless I misunderstand the documentation (I did not read all of it), vmatch searches for local matches and clusters by that. If I understand correctly it might be possible to fo ...
written 21 months ago by lelle780
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Comment: C: Clustering PacBio CCS reads
... Thanks for the suggestion. It seems the clustering would be based on local alignments/matches. I need something that takes into account the full sequences. I would also prefer to use free (as in freedom) or at least open source software. ...
written 21 months ago by lelle780

Latest awards to lelle

Scholar 16 months ago, created an answer that has been accepted. For A: What kind of accession code is NP_000123.1?
Popular Question 21 months ago, created a question with more than 1,000 views. For Scaffolding Without Paired Read Information
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Scholar 4.0 years ago, created an answer that has been accepted. For A: Can Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline so t
Scholar 4.4 years ago, created an answer that has been accepted. For A: Can Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline so t
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Voter 4.5 years ago, voted more than 100 times.
Supporter 4.8 years ago, voted at least 25 times.
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Getting The Number Of Chromosome From Gene Id For A Lot Of Genes
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Tools For Rad-Seq Data
Teacher 6.4 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)

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