User: cjain

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cjain0
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Posts by cjain

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PAR-CLIP data analysis
... Hi: Do you have a suggested pipeline for the analysis of PAR-CLIP data (cross-linking and immunoprecipitation of protein-bound RNAs that contain a photoactivable nucleotide)? Thanks, C. Jain ...
clip-seq rna-seq written 9 days ago by cjain0 • updated 6 days ago by Bjoern Gruening4.6k
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Variant analysis help
... Hello, I am trying to identify variants using data from a BAM file generated from an RNA-Seq experiment (not DNA-seq). I first tried to do so by making a pileup file using the BAM file as an input and a reference genome that I provided. When I tried to filter the pileup file, that command did not g ...
rna variants snp written 4 months ago by cjain0 • updated 4 months ago by Jennifer Hillman Jackson22k
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RNA genes count using HTseq
... Hello: I am new to Galaxy, but based on my understanding of how things work, I mapped some RNA-seq data from E. coli K-12 onto a reference genome obtained via UCSC using Bowtie, and then ran that through HTSeq to get a count of reads for the different genes. All of that worked well, but what was mi ...
htseq_count reference-annotation reference-genome written 8 months ago by cjain0 • updated 8 months ago by Jennifer Hillman Jackson22k
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Downloading GFF files from NCBI
... Hi: Can someone help me figure out how to import a genome from the NCBI website into Galaxy in a GFF (or GTF) format? I would like to use HTSeq to quantify our RNA-seq reads onto the downloaded genome. Thanks, Chaitanya Jain ...
rna-seq written 8 months ago by cjain0 • updated 8 months ago by Jennifer Hillman Jackson22k

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