User: filippo.martignano

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Posts by filippo.martignano

<prev • 14 results • page 1 of 2 • next >
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Comment: C: db-GaP / GTEx analysis on the cloud. Easiest way?
... Thanks! Yep I knew about AnVIL, but (probably I'm doing it wrong) it seems to allow you only to use the "standard workflows" they provide, and not to use a custom one. There is a link to dockerstore for "additional workflow" but I cannot find a way to import one in my workspace. Also, I'm interested ...
written 4 weeks ago by filippo.martignano10
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db-GaP / GTEx analysis on the cloud. Easiest way?
... Hi! I would like to analyze db-GaP data (in particular GTEx data); since i need to analyse WGS bams (600 samples), the total size would be overwhelming, so I wanted to do the analysis on the cloud. Can anyone suggest me a platform that allows me to both use my own tools/pipeline and to get the fil ...
db-gap cloud amazon gtex google written 4 weeks ago by filippo.martignano10 • updated 4 weeks ago by i.sudbery6.4k
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Alignment of short sequences allowing gaps and wildcards
... Hi everybody! I have sequenced some DNA fragments (with nanopore) that had been previously barcoded with a barcode like this: > AATACGACTCACTATAGNNNNNNNNNNTATCCTCANNNNNNNNNNCTATAGTGTCACCTAAA so basically it is made by 3 different barcodes separated by 10 random nucleotides: Barcode1 - 10Ns - ...
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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 18 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 18 months ago by filippo.martignano10 • updated 6 months ago by phaedragius0
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Comment: C: Jitterbug, mobile element tool, docker container
... unfortunately they don't seem to support python3... ...
written 18 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 18 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 19 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 2.1 years 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 2.1 years ago by filippo.martignano10

Latest awards to filippo.martignano

Popular Question 8 months ago, created a question with more than 1,000 views. For Samtools mpileup: AF1 and DP4 not provided
Popular Question 8 months ago, created a question with more than 1,000 views. For GTEx bam/vcf files download
Popular Question 13 months ago, created a question with more than 1,000 views. For Creation of a large Panel of Normals for Mutect2 analysis

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