Moderator: Rob

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Rob3.4k
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@nomad421
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34 minutes ago
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8 years, 6 months ago
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Posts by Rob

<prev • 221 results • page 1 of 23 • next >
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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 11 weeks ago by Rob3.4k
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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 3 months ago by Rob3.4k
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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 4 months ago by Rob3.4k
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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 4 months ago by Rob3.4k
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Comment: C: Understanding salmon codes
... That's a very surprising difference if the annotations are really the same. Would you be able to share the reads from one of your samples? We'd be interested to take a look. ...
written 4 months ago by Rob3.4k
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Comment: C: Understanding salmon codes
... Hi Morris, Can I ask how you verified that these are "human"? I took the sequences you gave above, and searched against the gencode transcriptome using Bowtie2 as the aligner. Both of these reads came back as completely unmapped. I did get a hit with blast (https://www.ncbi.nlm.nih.gov/nucleot ...
written 4 months ago by Rob3.4k
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Comment: C: Understanding salmon codes
... Hi Morris, It looks like you have a big space between the `--` and the flag name that should follow immediately after. That is, your command line should be: ``` salmon quant -i gencode_v29_idx -l A -1 Treated_1_m1.fastq -2 Treated_1_m2.fastq -p 4 --validateMappings --writeUnmappedNames -o salmo ...
written 4 months ago by Rob3.4k
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Comment: C: Understanding salmon codes
... Actually, salmon can accept gzipped FASTA files for reference index creation as well as gzipped FASTA/Q files for quantification. I believe that Morris was able to build the index, but is running into problems while quantifying. ...
written 4 months ago by Rob3.4k
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Answer: C: Understanding salmon codes
... Hi Morris, You should add the index *directory* as the parameter to `-i`, so, try: ``` (salmon) [@ws7910 RNAseq]$ salmon quant -i gencode_v29_idx -l A -1 Treated_1_m1.fastq -2 Treated_1_m2.fastq -p 4 --validateMappings -o salm_treated1 ``` I've also removed a spurious `/` before `gencode_v29_idx ...
written 4 months ago by Rob3.4k
0
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Comment: C: Salmon transcriptome generation
... Hi Morris, The `-k` argument has a default value (31) that is used if `-k` is not provided. I you wish to use the default, you don't have to pass that option explicitly. If you want to use another value of k, then you can pass that to the index command. ...
written 4 months ago by Rob3.4k

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