User: skhan

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skhan20
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Posts by skhan

<prev • 7 results • page 1 of 1 • next >
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(Closed) CLI tool to extract FASTA sequence from a .ab1 file
... Hi there, I have a few hundred .AB1 files, with their associated .PHD.1 files. I can successfully open each .AB1 files in UGene as well as FinchTV and extract a .SEQ file (plain FASTA file) manually. However, this involved a lot of mouse clicks. Does anyone know of command line tool for extracting ...
.ab1 written 4 weeks ago by skhan20
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Which reference to map against for RNA-Seq using HISAT2
... Hi all, I am trying to determine differential expression between two test conditions - in rat. The first step would be to map the sequencing data to a rat reference of some sort, and I would like to use HISAT2 (locally installed on my machine) along with the Ensemble rat genome. Which reference fi ...
hisat2 rna-seq written 3 months ago by skhan20 • updated 3 months ago by Jennifer Hillman Jackson24k
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Answer: A: BED file for Candida albicans
... Thanks Jen, that was tremendously helpful! A few things I learned along the way that may be helpful to others: - the candidagenome.org FASTA contains diploid info + sequence for what I think is the mitochondrial genome (chrM); the GenBank genome contains haploid sequences and no mitochondrial geno ...
written 4 months ago by skhan20
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BED file for Candida albicans
... Hi there, Does anyone know where I can get, or how I can generate, a BED file (or GTF file) for Candida albicans (strain SC5314, assembly version 22)? The current assembly is here but I'm not sure how to generate a BED file from the data there: http://www.candidagenome.org/download/sequence/C_alb ...
yeast gtf bed written 4 months ago by skhan20
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Answer: A: I can't find FreeBayes
... Thanks Nate. I used the tool from that link but my results (the position matches listed in the VCF, using hg19) don't agree with what I was getting before. I'll troubleshoot on my end. Just and FYI. ...
written 4 months ago by skhan20
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I can't find FreeBayes
... Hi all, Up until yesterday I was using FreeBayes and all was well. Today I can't find FreeBayes in Galaxy. I have a few workflows that use FreeBayes and these workflows no longer run either. Does anyone know what happened to FreeBayes? Has it been deprecated? Is if momentarily offline? Or am I exp ...
freebayes snp tool written 4 months ago by skhan20
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Comment: C: Rsync with G2 no options available
... "Rsync with g2" is behaving the same for me. Any chance it may have been replaced by a new tool yet? Thanks. ...
written 4 months ago by skhan20

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