User: skhan
skhan • 40
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- Last seen:
- 5 months ago
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- 1 year ago
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Posts by skhan
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... 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 ...
written 5 months ago by
skhan • 40
• updated
5 months ago by
Jennifer Hillman Jackson ♦ 25k
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... Are you using quotation marks in those file names? ...
written 6 months ago by
skhan • 40
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... 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. ...
written 6 months ago by
skhan • 40
• updated
6 months ago by
Jennifer Hillman Jackson ♦ 25k
1
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... 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 months ago by
skhan • 40
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... 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 months ago by
skhan • 40
1
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... Try uploading your file through the FTP service: https://galaxyproject.org/ftp-upload/ . ...
written 7 months ago by
skhan • 40
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... 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 ...
written 8 months ago by
skhan • 40
0
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1
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... 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 ...
written 11 months ago by
skhan • 40
• updated
11 months ago by
Jennifer Hillman Jackson ♦ 25k
1
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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 11 months ago by
skhan • 40
2
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... 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 ...
written 11 months ago by
skhan • 40
Latest awards to skhan
Scholar
7 months ago,
created an answer that has been accepted.
For A: Upload FASTQ in new version of galaxy
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