User: tassa.saldi
tassa.saldi • 0
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Posts by tassa.saldi
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... Just as an update for this post, I decided to filter the bam file for only unpaired reads (they were a mix and I was afraid that was the problem). I then filtered for reads only on the positive strand (so the only thing that could be in the file are (+) reads), but I am still getting several NAs an ...
written 7 months ago by
tassa.saldi • 0
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... Nice. I didn't know about the code option; I'll use that in the future. Thanks so much. ...
written 7 months ago by
tassa.saldi • 0
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... Hi all,
I am trying to count cryptic splicing junctions using the featureCounts `-J` option. The program is working great in that I am getting the same number of junctions in the output file as I see on the genome browser screen. However, a large number of my junction counts have a strand designa ...
written 7 months ago by
tassa.saldi • 0
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... Hello,
I'm wondering if anyone out there can help me. I am trying to calculate mean coverage over exons and introns in my RNAseq dataset using bedtools coverage -mean. I have very large bam files that are actually combined files from two sequencing runs- one single end and one paired-end. I am ha ...
written 22 months ago by
tassa.saldi • 0
• updated
22 months ago by
drkennetz • 480
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... Hello,
I went ahead and had BBtools installed on our university server (there is a lot of cool stuff in there!). I ran the the following command:
callvariants.sh in=C4_DMS_genome_merge_sorted.sam out=bbtools_out.txt ref=~/Datafiles/human/genome.fa ploidy=2 rarity=0.00001 clearfilters (also tried r ...
written 3.0 years ago by
tassa.saldi • 0
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... Awesome! I will give it a try. Thanks! ...
written 3.0 years ago by
tassa.saldi • 0
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... Hi,
Not sure how helpful this is, but I think the disappearing deletions and insertions are due to indels only being called for sites that do not have another type of mutation (i.e. mismatch).
Anyone know how to get mpileup and bcftools to report both an indel and a mismatch at the same site rega ...
written 3.0 years ago by
tassa.saldi • 0
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... Hello,
Does anyone out there have a simple script that can extract the positions of deletions from a sam file as a bed file (chromosome, start of deletion, end of deletion)?
Thanks in advance!
...
written 3.0 years ago by
tassa.saldi • 0
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... Hello,
Does anyone know how I can create a file that gives me coverage, mismatches, insertions and deletions from an RNAseq bam file? Pysamstats is not working as it counts spliced regions as deletions and the spliced region is also added to the coverage (both incorrect). I also cannot split the r ...
written 3.0 years ago by
tassa.saldi • 0
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... Hello,
I need to filter out reads from my sam files that contain deletions larger than 3bp. Does anyone know of a simple way to do that? I need to keep other low quality reads (like reads that contain small deletions, mismatches and insertions).
Thanks! ...
written 3.1 years ago by
tassa.saldi • 0
• updated
3.1 years ago by
Pierre Lindenbaum ♦ 128k
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