User: ctseto

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ctseto280
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Posts by ctseto

<prev • 45 results • page 1 of 5 • next >
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Comment: C: How can both pairs in paired-end sequencing data be aligned to the forward stran
... Indeed, sometimes the mappings are a bit perplexing. One option if you have downstream plans is to pick out only the reads that have a particular combination of flags for your downstream analysis? It is tempting to just pick out the ones that are "mapped" or "unmapped" (mapped to your desired contig ...
written 10 weeks ago by ctseto280
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Comment: C: How can both pairs in paired-end sequencing data be aligned to the forward stran
... Same on my end, though my use case was mapping PE reads to the contigs which were generated from their de novo assembly. Definitely very strange... ...
written 10 weeks ago by ctseto280
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Comment: C: How can both pairs in paired-end sequencing data be aligned to the forward stran
... I would assume 67 should be 83 or 99 (read reverse or mate read reverse) and 131 would be 147 or 163 (read reverse or mate reverse) ...
written 11 weeks ago by ctseto280
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Comment: C: How can both pairs in paired-end sequencing data be aligned to the forward stran
... For my own data, lots of 83/163 (read paired, mapped in proper, reverse strand, first && read paired, mapped in proper, mate_reverse_second in pair) and 99/147 (paired/proper/reverse/second && paired/proper/mate_reverse/first); assembly with megahit, mapping with BWA. I'm just par ...
written 11 weeks ago by ctseto280
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Comment: C: How can both pairs in paired-end sequencing data be aligned to the forward stran
... There's a few cases where you'll definitely want to check the alignments by hand. That said, I tend to regard "properly" with a bit of suspicion. 67/131 only trip read_is_paired/in_proper_pair and R1 | R2 with neither being "reverse strand", which has interesting implications about orientation. You ...
written 11 weeks ago by ctseto280
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Comment: C: Megahit assembly fasta header question
... Thanks! how did I miss that? ...
written 11 weeks ago by ctseto280
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Answer: A: How can both pairs in paired-end sequencing data be aligned to the forward stran
... I suspect a lot of this boils down to how the sam flags are assigned and spec'd by the aligner. Even the whole "properly" thing involves some handwavium. ...
written 11 weeks ago by ctseto280
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Megahit assembly fasta header question
... Running megahit, and attempting to parse some information from the assembly (such as "coverage"). For a header like > Sample_k141_28 flag=1 multi=4.0000 len=1042 What is flag? and multi? ...
megahit written 11 weeks ago by ctseto280 • updated 11 weeks ago by RamRS25k
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Comment: C: kraken2 different bacteria read counts on custom database
... My interpretation here is that db two without human classifies human as "0" (unclassified. It seems it is 131567 /or/ 1280, depending on the database; at least for Read1 In read2 it is either 9606 or 2759, in your database sans human 0 or 1280. In read 2 the first 21 kmers are human; without human ...
written 4 months ago by ctseto280
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... I'm guessing Kraken1, as you mention bacteria | virus | plasmid, which I vaguely remember are the databases used in Kraken1. ...
written 4 months ago by ctseto280

Latest awards to ctseto

Voter 11 weeks ago, voted more than 100 times.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to determine species of paired-end .fastq files (low mapping rates and incon
Supporter 9 months ago, voted at least 25 times.

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