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Reads are the sequences output by a sequencing machine after the raw signal (e.g. light, electricity) is converted into bases by a basecaller.

1
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It's common for assemblers to have a coverage threshold to make sure that there are enough reads across the same region to properly assemble a contig. … If your overlap were representative (e.g. a heterozygous variant in a diploid genome, based on a few tens of reads of 100bp, rather than 6bp), then the resulting assembly would have a bubble in the assembly …
answered Oct 22 '17 by gringer
6
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mapped: 2341 SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped SN reads unmapped: 51 SN reads properly paired: 0 # proper-pair bit set SN reads paired: … 0 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 SN total …
answered Oct 1 '17 by gringer
1
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To emphasise the issue (as outlined in the 1/n update), consider an input file with one record that is 5 million bases long, and one records that is 100 bases long. You want an equal probability of se …
answered Jun 19 '17 by gringer
3
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Sequencing failure When reads don't map across the variant region, then it's impossible to accurately determine a genotype for that region. …
answered Jun 13 '17 by gringer
2
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This is quite a similar question to this one, but I notice that you're specifically asking about a probability distribution rather than differential expression. That sounds like gene dispersion and/or …
answered Apr 28 '21 by gringer
2
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Answer from @ATpoint, converted from comment: A detected gene is one that has a count > 0, and generally the deeper you sequence the more genes you detect until you reach a saturation which is being i …
answered Jun 20 '21 by gringer
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some code a couple of years ago for assigning read groups based on variants at particular locations; this was set up for HIV variant splitting, so I expect it should also work on SARS-CoV-2 nanopore reads … You'd use it as follows: samtools view -h mapped_reads.bam | \ samVarSplitter.pl [-ref <refName>] [-pos <int>] | \ samtools sort > grouped_reads.bam Then the reads can be split into different files …
answered May 27 '21 by gringer