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Forum: Bioinformatics 10-26-2021, 12:44 AM
Replies: 0
Views: 492
Posted By pitch_
Obtaining GVCF from bam files

Dear all,

My aim is to identify Runs of Homozygosity(ROH) in my samples. I kept getting 0 ROHs in both Plink and detectRUNs softwares from ANGSD output. I assume this is because the tped files I...
Forum: Bioinformatics 03-10-2020, 01:40 AM
Replies: 0
Views: 1,007
Posted By pitch_
Calculating per site Dxy

Hi everyone,

I am trying to calculate Dxy per site between two populations from ANGSD output. I am using the CalcDxy.R script from NGSpopgen for this purpose. I seem to be getting really high Dxy...
Forum: Bioinformatics 03-25-2019, 12:50 AM
Replies: 6
Views: 1,403
Posted By pitch_
Hi all, After checking the fragment size and...

Hi all,

After checking the fragment size and mapping, I found that both of you were right, the coverage pattern is due to overlap of read 1 and read 2.

Thanks for the help! :)
Forum: Bioinformatics 03-20-2019, 08:55 AM
Replies: 6
Views: 1,403
Posted By pitch_
They are paired-end reads with a read length of...

They are paired-end reads with a read length of 150bp sequenced on illumina Hiseq4000 platform.

The insert size determined by qualimap for the 2 samples are
1st: 4194.82
2nd: 33,264.66
I am...
Forum: Bioinformatics 03-18-2019, 09:13 PM
Replies: 6
Views: 1,403
Posted By pitch_
Hi Luc, that does sound like a plausible reason....

Hi Luc, that does sound like a plausible reason. What other info would help in confirming it?
Forum: Bioinformatics 03-18-2019, 10:59 AM
Replies: 6
Views: 1,403
Posted By pitch_
Strange coverage histogram of museum samples

Hi everyone,

I had sequenced ancient museum samples on Illumina Hiseq 4000 platform. After running through typical pre-processing steps to generate a bam file (eg. cutadapt, bwa mem, mark...
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