User: heso

gravatar for heso
heso40
Reputation:
40
Status:
New User
Location:
Sweden
Last seen:
6 months ago
Joined:
3 years, 9 months ago
Email:
h*******@gmail.com

Posts by heso

<prev • 11 results • page 1 of 2 • next >
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Comment: C: bbduk fails to output histograms for random files
... It indeed was a memory issue. Didn't suspect this as the details that Slurm gave didn't indicate to memory shortage. But problem fixed now. Thanks! ...
written 6 months ago by heso40
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bbduk fails to output histograms for random files
... Hi, I'm having a problem with running bbduk on the server on a range of fastq.gz files (unpaired). Over a range of 24 files, 4 random files fail to get the histogram outputs. I do receive the fastq filtering (quality trimming+length filtering) output files, but even then I guess can't be sure that ...
bbduk bbtools written 6 months ago by heso40
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Where/how to get population specific AF for a set of SNPs
... Hi, I'm trying to retrieve population specific (EUR) allele frequencies for a few hundred SNPs I got from the GWAS Catalog. Somehow, I can't find any of those SNPs in the 1000 genomes vcf file ( ftp://ftp.ensembl.org/pub/release-91/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz), but searchi ...
allele frequency snp written 22 months ago by heso40 • updated 22 months ago by Nicolas Rosewick9.0k
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Comment: C: AWK: if value falls within a range, print sum of values
... This worked perfectly! Thanks a lot for the time and effort :) ...
written 2.9 years ago by heso40
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Comment: C: AWK: if value falls within a range, print sum of values
... Thanks for the reply! I don't seem to get it to work though (no output). I think `if($7>=$2 && $7<=$3)` should rather be `if($8>=$2 && $8<=$3)` but even that does not solve the issue... ...
written 2.9 years ago by heso40
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AWK: if value falls within a range, print sum of values
... I've got two sorted tab-delimited files: input.txt includes chromosome, location, gene name, strandedness input.txt 10 282035 282125 RNA1 - 10 4134522 4134564 RNA1 - 10 5299783 5299910 RNA2 - 10 5900317 5900359 RNA1 - ...
awk written 2.9 years ago by heso40 • updated 2.9 years ago by Alex Reynolds30k
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Comment: C: How to subset a FASTQ file based on a list of sequences
... I do have command line experience. Can you suggest a code? ...
written 3.4 years ago by heso40
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How to subset a FASTQ file based on a list of sequences
... I have a file1.txt (one sequence per line) which I want to use as a reference to filter out entries from a file.fastq. To clarify, I want to keep the file.fastq entries that perfectly match the sequences in file1.txt I know BBMap has filterbyname.sh for filtering by ID's. Is there some tool that I ...
fastq filter written 3.4 years ago by heso40 • updated 3.4 years ago by Jake Warner810
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How to calculate the sum of ranks per gene??
... Hi, I've got a table with ranked miRNAs from different samples. sample1 sample2 sample3 sample4 sample5 1 mmu-mir-21a mmu-mir-140 mmu-let-7i mmu-let-7i mmu-mir-218-2 2 mmu-mir-143 mmu-let-7i mmu-mir-27b mmu-let-7f-2 mmu-mir-143 3 mmu-let-7f-2 mmu-mir-1 ...
rna-seq written 3.5 years ago by heso40 • updated 3.5 years ago by Tom_L320
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Comment: C: Where Can I Download Pirna (Piwi Rnas) Of Mouse (Mm9)
... Worked perfectly, thanks a lot :) ...
written 3.7 years ago by heso40

Latest awards to heso

Popular Question 19 months ago, created a question with more than 1,000 views. For How to subset a FASTQ file based on a list of sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For How to calculate the sum of ranks per gene??
Popular Question 22 months ago, created a question with more than 1,000 views. For AWK: if value falls within a range, print sum of values

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