User: filippo.martignano

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Posts by filippo.martignano

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Splice junction sites and number of splitted reads from STAR aligned bam
... Thank you very much Eric! I did alread know about that thread, anyway it's a bit a "too much information" situation for me. I explain better: I'm looking for something as "raw" as possible (as I said, basically only the raw number of splitted read at a given position), all the tools I've checked out ...
written 9 months ago by filippo.martignano10
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Splice junction sites and number of splitted reads from STAR aligned bam
... Hi everyone! I'm working with some RNA-seq bams aligned with STAR. What I want to do is to detect splicing sites (both known and unknown) along with the coverage information (basically how many reads are spliced at a given position) Basically I'm looking for a tool that does exactly what "sashimi ...
sashimi plot rna-seq splice junctions written 9 months ago by filippo.martignano10 • updated 9 months ago by trausch1.2k
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Comment: C: Jitterbug, mobile element tool, docker container
... unfortunately they don't seem to support python3... ...
written 10 months ago by filippo.martignano10
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Jitterbug, mobile element tool, docker container
... Hi everyone, I recently started using this tool for the detection of mobile elements insertion: https://github.com/elzbth/jitterbug I wanted to use it through the https://cgc.sbgenomics.com/ platform, but to do so the tool should be loaded on a docker container. I tried to load it by myself, unfor ...
jitterbug docker mobile elements written 10 months ago by filippo.martignano10
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GTEx bam/vcf files download
... Hello. I would like to use GTEx DNA & RNA-seq data. from the download section (https://www.gtexportal.org/home/datasets) it seems that both aligned .bam files and .vcf files are available, but it says to download the files through dbGAP, and on dbGAP I was able to find only SRA unaligned runs. ...
vcf bam gtex written 10 months ago by filippo.martignano10
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Comment: C: Samtools mpileup: AF1 and DP4 not provided
... I was using .bam files from Genome In A Bottle project, i belive they are aligned with novalign. I just tried also with TCGA samples that are aligned with BWA (if I am correct) and these are the results: chr10 47663 . C T 218 . DP=86;ADF=10,19;ADR=0,41;AD=10,60;DPR=10,60;VDB=0.923183;SGB=-0.693147; ...
written 16 months ago by filippo.martignano10
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Comment: C: Samtools mpileup: AF1 and DP4 not provided
... Hi! Thanks a lot, unfortunately it still doesn't provide such information. Is it possible that it is because I generated a VCF with samtools mpileup instead of a BCF like you did? That doesn't actually make sense to me, but it seems to be the only difference in the pipeline. ...
written 16 months ago by filippo.martignano10
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Samtools mpileup: AF1 and DP4 not provided
... Hello! I'm using this command line: samtools mpileup SAMPLE.bam -f GENOME.fasta -B -d 1000 -R -Q 20 -l BEDFILE.bed -t ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -v > OUTPUT.vcf and the resulting VCF lines look pretty much like this: chr2 70000005 . T G,<*> 0 . DP=64;ADF=29,0,0;ADR=23,3,0;AD=5 ...
samtools mpileup af1 info written 16 months ago by filippo.martignano10 • updated 16 months ago by Kevin Blighe39k
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suggested value for SP (Phred-scaled strand bias P-value) Samtools mpileup
... Hi everyone! i'm setting up the --output-tags in my samtools mpileup command line. I want also to include SP (Phred-scaled strand bias P-value), according to the samtools documentation (http://www.htslib.org/doc/samtools-1.3.html) it seems that SP needs a value inside the square brackets. in the do ...
sp samtools strand bias mpileup written 17 months ago by filippo.martignano10
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Truth sets for variant calling validation
... Hi everyone! I was looking for validated truth sets in order to test my custom pipeline for variant calling. I've already found the ICGC-TCGA DREAM truth sets ( https://www.synapse.org/#!Synapse:syn312572/wiki/62018 ), and the genome in a bottle truth sets (http://jimb.stanford.edu/giab). Can you ...
variant calling validation truth sets written 17 months ago by filippo.martignano10 • updated 17 months ago by Kevin Blighe39k

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