User: cjain

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cjain0
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Posts by cjain

<prev • 6 results • page 1 of 1 • next >
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Read counts for limited genome regions
... Hello: I would like to get raw reads depth at each genome position for a limited region of the chromosome. What would be the best tool to use and what is the correct format to limit the query region? Thank you, Chaitanya Jain University of MIami ...
bigwig bedtools htseq_count bamtools featurecount written 6 months ago by cjain0 • updated 6 months ago by Jennifer Hillman Jackson25k
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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 12 months ago by cjain0 • updated 12 months ago by Jennifer Hillman Jackson25k
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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 13 months ago by cjain0 • updated 13 months ago by Jennifer Hillman Jackson25k
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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 17 months ago by cjain0 • updated 17 months ago by Jennifer Hillman Jackson25k
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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 20 months ago by cjain0 • updated 20 months ago by Jennifer Hillman Jackson25k
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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 21 months ago by cjain0 • updated 21 months ago by Jennifer Hillman Jackson25k

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