User: jh

gravatar for jh
jh30
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30
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New User
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Last seen:
6 months ago
Joined:
4 years, 5 months ago
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j**********@hotmail.com

Posts by jh

<prev • 14 results • page 1 of 2 • next >
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allele frequency bcf tools
... Hi, I would like to get the read counts for the ref and alt allele in a vcf file using bcf tools call. I use this command: bcftools mpileup -Ou -f genome.fa {input.bam} | bcftools call -m -o {output.vcf} But I don't see the counts for the alt allele in the output, only total DP. Any a ...
variant calling snp written 6 months ago by jh30 • updated 6 months ago by Kevin Blighe67k
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Redirect output from MIXCR
... Hi, I am including MIXCR in a snakemake pipeline, and would like to know how to redirect the output files to a specified path. I can't seem to find this info in the documentation. https://mixcr.readthedocs.io/en/master/quickstart.html Does anyone know? Thanks in advance ...
rna-seq written 19 months ago by jh30 • updated 9 weeks ago by mrkt0
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Comment: C: Reference for Salmon
... Thank you so much!! :D ...
written 3.3 years ago by jh30
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Comment: C: Reference for Salmon
... Rob: Which transcriptome reference file do you recommend I build the index from? And where can I get such files? :) I want to analyze two different outputs: (1) isoforms of known genes in the human genome, and (1) total transcript abundance of known genes in the human genome with HGNC gene names. ...
written 3.3 years ago by jh30
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mitcr java error
... Hi! I want to pull out Tcell receptors from Tcell WGS data using mitcr and the following command java -Xmx50g -jar mitcr-1.0.3.jar -pset flex -gene TRB sample.r1.fq.gz sample_r1.txt i get the following java error: Initialisation: progress unknown Individual sequence analysis & cl ...
tcell sequencing wgs mitcr written 3.4 years ago by jh30 • updated 3.4 years ago by genomax92k
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Reference for Salmon
... Hi, With Salmon, reads are mapped against the transcriptome and not the genome. Is it possible to use an extracted transcriptome from the human genome prepared for RSEM? Thanks! ...
rna-seq written 3.4 years ago by jh30 • updated 3.4 years ago by Rob4.5k
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(Closed) The cause of frameshift mutations
... Hi! Indels cause frameshift mutations. Can a missense mutation cause a frameshift, such that a mutation results in the sequence AUG to be present earlier in the transcript than the start codon. Thanks! ...
genome written 3.8 years ago by jh30
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Comment: C: (ERR): bowtie2-align exited with value 141
... I installed a previous version, bowtie2 2.2.6 and then it worked! So the 141 error seems to be a bug in the 2.2.8 release. Thanks! ...
written 3.9 years ago by jh30
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Comment: C: (ERR): bowtie2-align exited with value 141
... Thanks Medhat! Can you please post the link where it says that 141 was a bug? I installed Bowtie2 2.2.8 as a conda package and the next release 2.2.9 doesn't exist as a conda package :( ...
written 3.9 years ago by jh30
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Comment: C: (ERR): bowtie2-align exited with value 141
... Hi! Thanks for fixing locale advice. (i'm working on linux yes) I'm running Bowtie2 2.2.8 ...
written 3.9 years ago by jh30

Latest awards to jh

Great Question 19 months ago, created a question with more than 5,000 views. For Repeat masker bed file
Popular Question 19 months ago, created a question with more than 1,000 views. For Reference for Salmon
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Reference for Salmon
Popular Question 2.6 years ago, created a question with more than 1,000 views. For (ERR): bowtie2-align exited with value 141
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Repeat masker bed file

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