User: tassa.saldi

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Posts by tassa.saldi

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Answer: A: featureCounts junctions giving me NA for junction strand
... 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 15 months ago by tassa.saldi0
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Comment: C: featureCounts junctions giving me NA for junction strand
... Nice. I didn't know about the code option; I'll use that in the future. Thanks so much. ...
written 15 months ago by tassa.saldi0
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featureCounts junctions giving me NA for junction strand
... 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 ...
rna-seq written 15 months ago by tassa.saldi0
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bedtools bamtobed of mixed paired-end and non-paired datasets
... 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 ...
rna-seq written 2.5 years ago by tassa.saldi0 • updated 2.5 years ago by drkennetz510
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Comment: C: SAMtools mpileup and bcftools doesn't call InDels...
... 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 3.7 years ago by tassa.saldi0
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Comment: C: SAMtools mpileup and bcftools doesn't call InDels...
... Awesome! I will give it a try. Thanks! ...
written 3.7 years ago by tassa.saldi0
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Answer: A: SAMtools mpileup and bcftools doesn't call InDels...
... 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 3.7 years ago by tassa.saldi0
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Extract bed file of deletions
... 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! ...
alignment rna-seq snp sequencing written 3.7 years ago by tassa.saldi0
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Per base statistics on an RNAseq bam file
... 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 ...
alignment rna-seq snp written 3.7 years ago by tassa.saldi0
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Filter sam file to remove reads with large deletions
... 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! ...
rna-seq written 3.8 years ago by tassa.saldi0 • updated 3.8 years ago by Pierre Lindenbaum132k

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