Moderator: Rob
Rob ♦ 3.6k
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Posts by Rob
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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
Rob ♦ 3.6k
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... 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 ...
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... 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 ...
written 10 weeks ago by
Rob ♦ 3.6k
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... 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
Rob ♦ 3.6k
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... 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
Rob ♦ 3.6k
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... 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
Rob ♦ 3.6k
3
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... 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
Rob ♦ 3.6k
1
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2
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... 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
Rob ♦ 3.6k
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... 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
Rob ♦ 3.6k
0
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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
Rob ♦ 3.6k
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For A: Can pairwise global alignment be done in linear memory with affine gap penalties
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For A: Can pairwise global alignment be done in linear memory with affine gap penalties
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