User: hopedwall

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hopedwall0
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Posts by hopedwall

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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
... Thanks, I'll give it a try! I'm working on Alternative Splicing event detection from paired-end samples and figured the average insert size might be useful. ...
written 9 weeks ago by hopedwall0
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
... I'm using [this repository][1] to generate rna-seq paired-end samples, from gene ENSG00000280145, human chromosome 21. Since I'm running BBMap locally on my machine, I needed shorter reads. [1]: https://github.com/davidliwei/RNASeqReadSimulator ...
written 9 weeks ago by hopedwall0
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
... I used BBMap in this way: bbmap.sh in=read_1.fa in2=read_2.fa ref=genome.fa out=bbout.sam I'm using simulated reads, generated from a single gene. Could this be the issue? What surprises me is that the value returned by samtools is completely different from the one returned by BBMap. I need th ...
written 9 weeks ago by hopedwall0
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
... Sorry about that, I'll edit asap! [edit: done] ...
written 9 weeks ago by hopedwall0
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Comment: C: BBMap and Samtools show different values for mean inner distance between mate pa
... Sure, here it is. BBMap output: Pairing data: pct pairs num pairs pct bases num bases mated pairs: 47.9200% 9584 47.9200% 1916800 bad pairs: 51.3550% 10271 51.3550% 20 ...
written 9 weeks ago by hopedwall0
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BBMap and Samtools show different values for mean inner distance between mate pairs
... I'm working on a project that uses paired-end samples where the inner distance between mate pairs is not provided, so I tried using BBMap (as suggested in other posts) in order to get an estimate. However, when I tried using samtools like this `samtools stats output.sam | grep "insert size average"` ...
next-gen rna-seq written 9 weeks ago by hopedwall0

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