User: AidanQuinn

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AidanQuinn30
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United States
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http://www.AidanQuinn....
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21 hours ago
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4 years, 5 months ago
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Posts by AidanQuinn

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Chromvar for single cell ATAC seq
... Do you have single cell mRNA expression and genome accessibility in the same cells?? If not, you'll need to think carefully about how you are clustering your cells and mapping clusters in one space to those in the other (i.e. how do you say that one RNA-seq cluster of cells is biologically equivalen ...
written 4 days ago by AidanQuinn30
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Comment: C: How to download raw sequence data from GEO/SRA
... This line works really well, thank you! A note on parallel; you can just add the -n 1 -P $nCores arguments to xargs. For example I used: esearch -db sra -query PRJNA515945 | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | xargs -n 1 -P 12 fastq-dump --split-files --gzip --skip-technic ...
written 4 days ago by AidanQuinn30
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Answer: A: GSEA analysis with Mouse (Please give some comments..)
... Generally I use Ensemble Biomart (but you can substitute your favorite gene ID conversion tool here) to convert all of the gene names in each gene signature in the *.gmx or *.gmt, from human to mouse. I then use the mouse IDs to make a custom *.gmx or *.gmt file. It's convenient to do this in R if ...
written 2.0 years ago by AidanQuinn30
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Extract MAF regions (transcripts) using GTF of exons
... Hello, I am interested in extracting multiple species alignment for a subset of species included in the UCSC multiz100way whole genome alignment. My GTF file contains exons, but ultimately I'd like to stitch together the full length transcripts and obtain FASTA formatted alignments for each transcr ...
maf multiple species alignment phast galaxy written 3.5 years ago by AidanQuinn30 • updated 3.5 years ago by natasha.sernova3.7k
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Answer: A: Tophat Error : Couldn't build bowtie index with err = 1
... I had the same problem today using the comprehensive gene annotation GTF from GENCODE and the Illumina pre-build genome. The file names were not the problem but the chromosome names were annotated differently in the GTF and the genome (*.fa) files. The GTF annotation for chromosomes was "chr#" and t ...
written 4.5 years ago by AidanQuinn30 • updated 4 weeks ago by RamRS25k

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Popular Question 18 months ago, created a question with more than 1,000 views. For Extract MAF regions (transcripts) using GTF of exons

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