Timeline for Diploid Consensus Sequences
Current License: CC BY-SA 4.0
9 events
| when toggle format | what | by | license | comment | |
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| Feb 12, 2021 at 1:24 | comment | added | annabelperry | @MaximilianPress Ah I have failed to clarify my end goal. I am designing a software for microsatellite detection from short-reads (no such software currently exists which meets my needs). I only want to call variants in "real" reads rather than duplicates. However, I have found an alternative to diploid consensus creation - I am instead going to run my software on short-reads (including duplicates) and use variant frequencies to filter out false positives. | |
| Feb 8, 2021 at 8:14 | answer | added | Fabio Marroni | timeline score: 1 | |
| Feb 6, 2021 at 14:57 | comment | added | Maximilian Press | This is a little hard to answer as is, could you give an example of the kind of data you want to get out? Do you want to phase the haplotypes, like in the linked paper? I think swbarnes2 has the right of it, that calling variants is the way to go. Also- duplicates are usually defined as reads with the same coordinates; unless you have very high coverage this is unlikely to remove more than a very small fraction of informative reads (they are more likely PCR or optical duplicates, i.e. artifacts). | |
| Feb 5, 2021 at 20:04 | comment | added | swbarnes2 | FWIW, I do not think that removing lines from a bam file is what you want to do at all. I think you need to be calling variants with phasing data, and using that vcf to make a modified fasta. A quick google turned this up biostars.org/p/225262 | |
| Feb 5, 2021 at 3:14 | history | edited | annabelperry | CC BY-SA 4.0 |
added 112 characters in body
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| Feb 5, 2021 at 3:10 | comment | added | annabelperry | @swbarnes2 I want to do what is described in this article, but I don't have PacBio long-reads to compliment my Illumina short-reads: doi.org/10.1093/bioinformatics/bty279 | |
| Feb 5, 2021 at 3:09 | comment | added | annabelperry | @swbarnes2 It's not that I want to simply remove the supporting reads - I should clarify my intent. My end goal is to use the consensus genome as input in a homebrew microsat-calling software. I don't want this software to call sequencing errors as microsats, so I want to merge all reads of the same sequence into a single consensus read based on base quality scores, generating two sets of sequences which are the pipeline's best guess at the individual's haplomes. I will edit my original post to make this clear. | |
| Feb 4, 2021 at 23:09 | comment | added | swbarnes2 | What you are asking for doesn't make sense. How on earth is any software supposed to determine if a discrepancy is a polymorphism or an error if you remove all the supporting reads? | |
| Feb 3, 2021 at 20:35 | history | asked | annabelperry | CC BY-SA 4.0 |