User: cjain

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cjain0
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Posts by cjain

<prev • 5 results • page 1 of 1 • next >
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Modifying GFF files
... Hi: I am working with a GFF file, which is missing 5' UTR annotations. I thought I might be able to add UTR data using the tools on Galaxy as follows: 1) Convert the existing GFF file to Excel format (.xls) using the pencil icon on Galaxy. 2) Download the Excel file and make changes. 3) Upload the ...
rna-seq written 8 weeks ago by cjain0 • updated 8 weeks ago by Jennifer Hillman Jackson22k
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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 ...
par-clip clip-seq rna-seq written 10 weeks ago by cjain0 • updated 9 weeks ago by Jennifer Hillman Jackson22k
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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 6 months ago by cjain0 • updated 6 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 10 months ago by cjain0 • updated 10 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 10 months ago by cjain0 • updated 10 months ago by Jennifer Hillman Jackson22k

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