User: skhan

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skhan30
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Posts by skhan

<prev • 13 results • page 1 of 2 • next >
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Checking coverage of yeast whole genome sequencing data
... I have WGS data (2x150b paired end NextSeq reads) for Yeast (sacCer3) and would like to know how much coverage the data has relative to the reference genome. My plan here is to use STAR to align the dataset to the reference (sacCer3), and then Qualimap to analyze the resultant BAM file. Is STAR th ...
yeast alignment star written 8 days ago by skhan30 • updated 8 days ago by Jennifer Hillman Jackson24k
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Comment: A: error on job submission using galaxy and slurm tool fastqc
... Are you using quotation marks in those file names? ...
written 6 weeks ago by skhan30
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How to prepare FastQ files for HISAT2
... Hi there, Should I be preparing or otherwise cleaning fastq files before I try to align them to a reference genome using HISAT2? If yes, how and using which tools? I have 2x 76 bases paired end (separate R1 and R2 files) reads and am attempting RNA-Seq. Thanks. ...
hisat2 rna-seq alignment fastq written 6 weeks ago by skhan30 • updated 6 weeks ago by Jennifer Hillman Jackson24k
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Answer: A: Galaxy HTSeq tool give zero counts
... I had this same problem. For me it turned out the chromosomes naming was different between the built-in rat genome I was using (e.g. "chr1"), and the GTF I had uploaded (e.g. "1"). ...
written 6 weeks ago by skhan30
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Answer: A: Visualisation of Fastqc charts
... If you run fastqc in terminal at e.g. `fastqc --outdir ~ file.fastq.gz` it will create, in your home directory (~), an html file that you can open with your favourite web browser to view graphs, as well as a .zip archive that you can extract and view .PNG image files using your favourite image viewe ...
written 6 weeks ago by skhan30
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Answer: A: Upload FASTQ in new version of galaxy
... Try uploading your file through the FTP service: https://galaxyproject.org/ftp-upload/ . ...
written 8 weeks ago by skhan30
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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 3 months ago by skhan30
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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 5 months ago by skhan30 • updated 5 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 6 months ago by skhan30
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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 6 months ago by skhan30

Latest awards to skhan

Scholar 8 weeks ago, created an answer that has been accepted. For A: Upload FASTQ in new version of galaxy

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