User: denis.k

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denis.k10
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2 months, 2 weeks ago
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d************@mail.utoronto.ca

Posts by denis.k

<prev • 4 results • page 1 of 1 • next >
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BAM -> FASTQ Conversion of CCLE data for STAR-Fusion. Filtering Steps?
... Hey everyone, I'm pretty new to RNA-seqencing and was wondering if anyone could help me out. I am trying to run a variety of SV callers (STAR-Fusion, etc.) on data from the CCLE (https://portal.gdc.cancer.gov/legacy-archive). Most SV Callers require .fastq files but all the data I have downloade ...
gene sequence rna written 16 days ago by denis.k10
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Cancer Cell Line WGS
... Hey Biostars! Was wondering if someone could help me out with this problem. I am looking for WGS data from cancer cell lines but have struggled to find any repositories online that store the BAM's or FASTQs. Does anyone have any insight on where I can look? Thank you in advance! ...
wgs next-gen sequencing written 4 weeks ago by denis.k10 • updated 4 weeks ago by ATpoint23k
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Comment: C: Issue With CRAM -> BAM -> FASTQ Conversion
... Thank you! It was a lib curl problem! Turns out that I just needed the --enable lib curl option. Such a silly problem. Thank you for all the help ...
written 4 weeks ago by denis.k10
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Issue With CRAM -> BAM -> FASTQ Conversion
... Please help! I am trying to obtain fastq files from the GDSC, all we have in the lab is CRAM files. Unfortunately, the reference genome seems to not exist when pulled from an online source. I have attempted to use the Samtools code which allows me to put in my own reference but I get an error messag ...
samtools fastq bam cram view written 10 weeks ago by denis.k10 • updated 9 weeks ago by jkbonfield180

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