Moderator: Rob

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Rob3.6k
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@nomad421
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8 years, 10 months ago
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Posts by Rob

<prev • 227 results • page 1 of 23 • next >
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Comment: C: Salmon error message
... Salmon's [parser](https://github.com/rob-p/FQFeeder) uses kseq under the hood, and it simply propagates the kseq error code if it encounters one. This [one](https://github.com/COMBINE-lab/salmon/blob/master/include/kseq.h#L204) seems to suggest that one of the files had a truncated quality string ( ...
written 24 days ago by Rob3.6k
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Answer: C: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
... STAR is a general purpose aligner. It can align reads to a genome or transcriptome, or whatever you provide. It can perform spliced alignment, and returns base-level alignments for the reads. These alignments can then be used for different purposes like being fed to transcript assembly tools, var ...
written 8 weeks ago by Rob3.6k • updated 8 weeks ago by genomax74k
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News: Testing and feedback of upcoming salmon release
... We are in the process of finalizing a new major release of [salmon](https://github.com/COMBINE-lab/salmon), and are looking for people willing to test [the latest (beta) releases](https://github.com/COMBINE-lab/salmon/releases) and give feedback. Though the command-line interface is largely identic ...
news salmon rna-seq written 10 weeks ago by Rob3.6k
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Comment: C: Python Program to read .fasta file to .txt file
... Do you just want to remove the header lines (i.e. the `> sequence_name` lines that appear before each sequence)? ...
written 10 weeks ago by Rob3.6k
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Comment: C: Merging the output of salmon for RNA-seq counting with paired-end and single-end
... There are a few ways to go about doing this technically. However, I would actually suggest _not_ merging the paired-end and single-end runs. Instead, I'd treat the sequencing protocol (SE vs PE) as a technical factor in the design matrix when you want to do differential testing in DESeq2. ...
written 3 months ago by Rob3.6k
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Comment: C: inconsistent results of rsem quantification
... The `-k 200` parameter does _not_ mean that "rsem will assign multiple alignment reads randomly." The `-k 200` parameter means that Bowtie2 will report up to 200 distinct alignments for a read, which RSEM will then determine how to probabilistically allocate in accordance with its model. When ther ...
written 3 months ago by Rob3.6k
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Answer: A: Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
... Hi Anthony, No; salmon does not use the PHRED score, either while mapping or aligning. The main reason for not using it during alignment or mapping is that it just tends not to be very useful for this purpose. If a nucleotide inside a reasonably long exact match is bad quality (and therefore lik ...
written 6 months ago by Rob3.6k
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Answer: C: do paired end reads both mapped to the same gene appear consecutive to each othe
... You might consider using `--no-discordant` and `--no-mixed` to avoid the complicated patterns that can occur when one alignment record (e.g. for read 1) is paied with multiple alignments (for read 2, or vice versa). Basically, for concordant alignments, Bowtie2 will fillow your expected format. Wi ...
written 7 months ago by Rob3.6k
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Answer: C: Salmon (quant.sf) to txtimport
... Hi Morris, In general, you should *not* modify the structure of the salmon directories as tximport relies on it. The easiest thing to do is to have a separate quant directory for each sample, and to provide those each to tximport using whatever naming convention you want for the quant *folders*. ...
written 8 months ago by Rob3.6k
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Comment: C: Understanding salmon codes
... How large are they? You could use a file-sharing website, or if it is easier, you should be able to upload the data to [this gdrive link](https://drive.google.com/drive/folders/17N35X4_-6yuR4JMfLpbcreDZhQow1jpM?usp=sharing). ...
written 8 months ago by Rob3.6k

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Scholar 9 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties
Scholar 9 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to handle Reverse complement in De-Bruijn Graph
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
Scholar 10 months ago, created an answer that has been accepted. For A: Can pairwise global alignment be done in linear memory with affine gap penalties

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