User: MaxF

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MaxF10
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Posts by MaxF

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Salmon Counts differ in Alignment and Quasi-Mapping mode
... Upon further testing, sorting the BAM file is the culprit. This must have been included by mistake in the pipeline I received. ...
written 5 days ago by MaxF10
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Comment: C: Salmon and reads order in fastq in quasi-mapping-based mode
... Upon further testing, sorting the file with samtools was the problem. ...
written 5 days ago by MaxF10
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Comment: C: Salmon Counts differ in Alignment and Quasi-Mapping mode
... Sorry, I forgot part of the pipeline. The BAM file was generated in star (unsorted) but then sorted by samtools: Here's the STAR arguments: --outSAMtype BAM Unsorted --outSAMattributes All --alignSJoverhangMin 8 --outSAMunmapped Within Here is the samtools run line: samtools sort -@ 8 - ...
written 6 days ago by MaxF10
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Salmon Counts differ in Alignment and Quasi-Mapping mode
... I am attempting to use Salmon (version 0.12.0) to quantify transcript counts from RNAseq data (unstranded paired-end reads). The existing pipeline in my lab is to trim/qc fastq files, align them with STAR (2.5.2a), merge sample BAMs together (if they were spread across lanes), sort them with samtoo ...
alignment salmon rna-seq written 6 days ago by MaxF10
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Comment: C: Salmon and reads order in fastq in quasi-mapping-based mode
... I used STAR in transcriptome mode (--quantMode TranscriptomeSAM), but I did align it against the hg38 genome. The text I was referring to is what ATpoint quoted: *"If your reads or alignments do not appear in a random order with respect to the target transcripts, please randomize / shuffle them bef ...
written 7 days ago by MaxF10
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Comment: C: Salmon and reads order in fastq in quasi-mapping-based mode
... This makes sense, but what about when putting BAM files directly into salmon? I've taken fastq files from the sequencer, aligned them with STAR and then sorted with samtools, and then put the sorted BAMs into salmon. The text from the Salmon doc indicates that this could be a problem, but I'm not s ...
written 7 days ago by MaxF10

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