User: lelle

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lelle740
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Berlin
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Posts by lelle

<prev • 73 results • page 1 of 8 • next >
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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 8 months ago by lelle740
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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 9 months ago by lelle740
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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 9 months ago by lelle740
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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 9 months ago by lelle740
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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 9 months ago by lelle740
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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 9 months ago by lelle740
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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 13 months ago by lelle740
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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 13 months ago by lelle740
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Clustering PacBio CCS reads
... I have a mock metabarcoding dataset that was sequence with PacBio. A 4.5kb long stretch of DNA was amplified and sequenced with Circular Consensus Sequencing. This means the error rate is around 1%, but a lot of these are indels. I want to cluster these sequences to create OTUs. What software would ...
pacbio clustering written 13 months ago by lelle740
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Answer: A: KEGG REST API
... You can use [Biopython][1]. [1]: http://biopython.org/DIST/docs/api/Bio.KEGG.REST-module.html ...
written 19 months ago by lelle740

Latest awards to lelle

Scholar 8 months ago, created an answer that has been accepted. For A: What kind of accession code is NP_000123.1?
Popular Question 12 months ago, created a question with more than 1,000 views. For Scaffolding Without Paired Read Information
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Scholar 3.3 years ago, created an answer that has been accepted. For A: Can Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline so t
Scholar 3.8 years ago, created an answer that has been accepted. For A: Can Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline so t
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)
Voter 3.8 years ago, voted more than 100 times.
Supporter 4.1 years ago, voted at least 25 times.
Teacher 4.6 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 4.8 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Tools For Rad-Seq Data
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Error When Running Fastx (Fastx_Quality_Stats)

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