User: dentepre

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dentepre0
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Posts by dentepre

<prev • 17 results • page 1 of 2 • next >
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Comment: C: bowtie - ebtw human index
... @genomax Yes, there is avalialbe ready index to download and it works, but I am not big fan of this kind of solution. To be honest, I am not completly sure if the version of genome which I use is completly the same as use for prebuild indexes. ...
written 5 weeks ago by dentepre0
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Comment: C: bowtie - ebtw human index
... @ATpoint Yes, I've tried to run bowtie using default settings. However, the file with human genome is larger than 4.0GB (the limit for "small" genome in bowtie) and bowtie generate .ebtwl files (for "large" genome). For kind of downstraem analysis, I need to have files with .ebtw extension. ...
written 5 weeks ago by dentepre0
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bowtie - ebtw human index
... Hi, I need index of human genome, but build by bowtie (version 1) and with .ebtw extension. How can I force bowtie to build "small" index of human genome? According to the manual, there is only option to force building "large" index from smaller genome. Thanks :) ...
next-gen written 5 weeks ago by dentepre0
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targeted resequencing data analysis
... Hi, I have to perform variant calling from DNA sequencing data, but in targeted sequencing mode. My libraries were enriched by set of about 100 genes and I want to find mutations (SNV and indels among them). What is the best way to perform this kind of analysis? Should I mapped to the whole refe ...
next-gen written 12 weeks ago by dentepre0 • updated 12 weeks ago by WouterDeCoster40k
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Comment: C: Best tool for variant calling
... Hi, can you show your script for whole pipeline (from fastq files)? ...
written 4 months ago by dentepre0
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selection of disease relevant pathways after NGS
... Hi, I need an advice. I work with rna-seq data obtained from intestinal cells from patients with IBD and healthy controls. I mapped raw reads to reference genome, obtained counts and performed differential expression procedures. As a results, I've obtained more that 200 genes, which expression is d ...
R rna-seq written 6 months ago by dentepre0
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tool for genome sequence manipulation
... Hi, I;m looking for genome-browse like tool. I need to have a possiblity to load genome from fasta file, select region by adding primer sequences and add genes and rs... snps/another mutations. Mostly for clinical genomic purpose. I know IGV, but there is no way to add for example primers as separa ...
genome sequencing written 8 months ago by dentepre0 • updated 8 months ago by oigl60
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Comment: C: human bwa indexed genome
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written 10 months ago by dentepre0
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human bwa indexed genome
... Hi, I need index of human genome created by bwa. I was tried to do it by myself (bwa index ...), but I have no memory to complete. Where can I find prebuild bwa index of human genome? Thanks, d. ...
next-gen written 10 months ago by dentepre0 • updated 10 months ago by finswimmer11k
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randfold - problem with installation
... Hi, I'm trying to install randfold from source, however there is still an error. /usr/bin/ld: cannot find -lsquid collect2: error: ld returned 1 exit status make: *** [randfold] Error 1 What should I do? ...
rna-seq written 23 months ago by dentepre0 • updated 23 months ago by Santosh Anand4.9k

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