Moderator: Rob
Rob ♦ 2.6k
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... So it's quite possible that there is not enough free memory to build the index with Bowtie2's default settings. You have only ~2.5x as much memory as the size of the input file, and this is likely a shared machine where other processes may be using memory. You can attempt to reduce Bowtie2's index ...
written 5 days ago by
Rob ♦ 2.6k
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... How much memory does the machine have? 100GB is quite large, so you'll need a reasonable amount of memory to even create the index. ...
written 5 days ago by
Rob ♦ 2.6k
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... There is no option in salmon directly equivalent to the `--sra-acc` option in HISAT. However, salmon will happily accept streaming input from a [fifo or named pipe](https://www.linuxjournal.com/article/2156). Hence, it should be possible to create a bash / snakemake / nextflow script to do the con ...
written 9 days ago by
Rob ♦ 2.6k
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... Hi [ATpoint](https://www.biostars.org/u/25721/),
Thanks for the detailed follow-up! It's good to see these empirical results, since it's my hope that the effect of the k-mer size wouldn't be too drastic in general. After all, the k-mer is used only as a seed, and the full matching is done again ...
written 9 days ago by
Rob ♦ 2.6k
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... Hi [ATpoint](https://www.biostars.org/u/25721/),
I would probably recommend going with the default kmer length down to the case where the shorter of the reads is 75bp, and then a smaller kmer size after that. As [h.mon](https://www.biostars.org/u/6093/) suggests, It's probably a good idea to incl ...
written 10 days ago by
Rob ♦ 2.6k
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... If you compare log2 fold change of exons to log2 fold change of transcripts, then no, it is _not_ meaningful. To have a meaningful comparison, you must be comparing the same targets of quantification. You cannot compare exon read counts to transcript read counts (or the fold-change of exon read co ...
written 20 days ago by
Rob ♦ 2.6k
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... The way you have described it, the answer is emphatically "no". You cannot compare transcript-level abundance estimates from salmon (or any other transcript-level abundance estimation tool) to exon-level quantifications from HTSeq in a meaningful way. The most reasonable comparison you could make ...
written 20 days ago by
Rob ♦ 2.6k
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Comment:
C: Salmon Algorithm Binary Search
... Salmon (in mapping based mode), uses an uncompressed SA aided by a hash table. HISAT uses a hierarchical FM-index (itself based on the BWT and the suffix array). ...
written 4 weeks ago by
Rob ♦ 2.6k
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... Hi Vincent,
The answer to your question is yes --- the mapping algorithm uses binary search --- but with two very important twists. First, it's important to note that the mapping algorithm augments the suffix array with a hash table. This hash table stores, for each k-mer, the _interval_ of the ...
written 4 weeks ago by
Rob ♦ 2.6k
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... Well, you should definitely filter on more specific tags to get rid of the alignments that don't map according to the library type, since salmon will discard them for quantification purposes. It's not easy to *discard* the multimappers. The fact that a multi-mapping reads maps to a particular locu ...
written 5 weeks ago by
Rob ♦ 2.6k
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