User: wolfgang.rumpf

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Posts by wolfgang.rumpf

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Answer: A: Kronagram from Kraken2 output?
... As it turns out the easiest solution was to use the raw kraken2 output (which normally gets dumped to standard out) and pipe that to the latest version of recentrifuge (0.28.9), which generates lovely kronagrams. ...
written 7 days ago by wolfgang.rumpf10
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Comment: A: Kronagram from Kraken2 output?
... I just run Kraken2 from the command line - the output typically looks like this: > 100.00 15885 0 R 1 root > 100.00 15885 0 R1 131567 cellular organisms > 100.00 15885 2 D 2 Bacteria > 38.89 6177 0 D1 1783272 Terrabacteria group > 27.10 4305 0 P 1239 ...
written 9 days ago by wolfgang.rumpf10
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Kronagram from Kraken2 output?
... I'm trying to build kronagrams (with KronaTools) from kraken2 output. Has anyone figured out a way of doing this? ...
kraken kronagram written 9 days ago by wolfgang.rumpf10
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Comment: C: Identify jumbled transcripts (scrambled exons) using HISAT2, stringtie, and GFFc
... Okay, that makes sense. But what about the downstream pipeline after minimap2? Was I right in assuming that stringtie and GFFcompare should show me jumbled/scrambled exons? ...
written 4 weeks ago by wolfgang.rumpf10
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Identify jumbled transcripts (scrambled exons) using HISAT2, stringtie, and GFFcompare?
... I have some PacBio RNA-seq data that should have a jumbled gene in it (e.g. the exons are not in the canonical order but instead go something like 1, 2, 3, 5, 6, 4, 5, 7, 8 etc - scrambled exons). I *thought* that by mapping my FASTQ with HISAT2 followed by mapping the resulting .bam to the referen ...
stringtie rna-seq gffcompare hisat2 written 4 weeks ago by wolfgang.rumpf10 • updated 4 weeks ago by danbileedg20190
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How can I filter my RNA-seq transcript data to display ONLY novel isoforms and variants?
... I have some RNA-seq data from (human) cancer cells and am trying to find non-canonical transcripts (e.g. splice variants, fusion products, etc.). I have already created a SAM/BAM file of the transcripts and retrieved accession information (using MagicBLAST), but now what I'd like to do is filter ou ...
fusion isoforms rna-seq splice-variant written 6 weeks ago by wolfgang.rumpf10 • updated 7 days ago by geek_y9.6k
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Biopython pairwise 2 - can I make it score an existing alignment?
... From Biopython, I can use pairwise2 to align two sequences and provide me with the score. Is there a way to get pairwise2 to NOT align, but to score an existing alignment? Essentially I'm looking for a way to do sum-of-pairs with a custom weight matrix (e.g. match = 1, indeed = -3, mismatch = -1). ...
pairwise2 python biopython alignment score written 10 months ago by wolfgang.rumpf10 • updated 11 weeks ago by Markus230
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Comment: A: How to go from Protein ID to EC number???
... We did download that database already and are working on that - thanks for the suggestion! But what we are seeing is that many of the PID's don't seem to have an equivalent EC - most of them, actually. P02647 is a perfect example. So clearly we're missing something! ...
written 2.4 years ago by wolfgang.rumpf10
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How to go from Protein ID to EC number???
... We have a dataset consisting of 580-some proteins and are trying to condense it down by functional group. As such we want to go from the existing Protein ID (e.g. P02647) to an EC number. I can't seem to find a reliable way of doing this, let alone doing it batch-wise. Any suggestions would be ap ...
ec pid protein protein id written 2.4 years ago by wolfgang.rumpf10 • updated 2.4 years ago by Elisabeth Gasteiger1.6k
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Comment: A: sequence in forward seq files but not in the reverse files
... Dan, I'm running into the same issue with my data in mothur.  I demultiplexed data that we received from Mr. DNA, and now have individual forward and reverse reads that I would like to contig together in mothur using make.contigs.  However, when I run make.contigs I get the same error as above ("... ...
written 3.3 years ago by wolfgang.rumpf10

Latest awards to wolfgang.rumpf

Scholar 7 days ago, created an answer that has been accepted. For A: Kronagram from Kraken2 output?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to go from Protein ID to EC number???

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