User: skumar53

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skumar5330
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2 months, 1 week ago
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s*******@jhu.edu

Posts by skumar53

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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... Thank you Devon and Jen for your insightful and informative replies! It truly went beyond the issue at hand and educated me further! About the issue, it can be likely that the genome was the issue : I had previously aligned to both the Chinese hamster 2013 genome and the Chinese Hamster Ovary 2017 ...
written 29 days ago by skumar5330
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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... I could just view my BAM file and these are the first few lines : @HD VN:1.0 SO:coordinate @SQ SN:AMDS01163391 LN:201 @SQ SN:AMDS01163392 LN:201 The entire file looks this way, with changing LN. FLAG, RNAME , POS, MAPQ, CIGAR, MRNM, MPOS, ISIZE, SEQ, QUAL, OPT all seem to be empty? Is ...
written 4 weeks ago by skumar5330 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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Comment: C: Featurecounts for paired end RNA-seq reads not generating counts
... Thanks for your reply Devon! I uploaded a GTF file and even compared 2 runs : one with mismatched genome version and the other with the right genome version and both gave me the same results. So I'm not sure what next to do. I viewed the GTF file in IGV and it does have chromosome start and end l ...
written 4 weeks ago by skumar5330
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Featurecounts for paired end RNA-seq reads not generating counts
... Hi I have paired end RNA-Seq reads that I aligned to my reference genome using HISAT2 (alignment mostly >90%) and obtained BAM files, as a result. When I tried to obtain count information for these BAM files using the annotated file of the same build of the reference genome, I find that the resu ...
hisat2 featurecounts rna-seq written 4 weeks ago by skumar5330 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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(Closed) Memory allocation error while trying to align paired end reads using RNA STAR
... Hi This is my first time using Galaxy for RNA Seq analysis. After uploading and normalizing my reference genome, I tried to align my paired-end fastq reads to this genome using RNA STAR. Unfortunately, the jobs failed with the error " This job was terminated because it used more memory than it was ...
hisat2 rna-seq alignment star memory written 9 weeks ago by skumar5330 • updated 9 weeks ago by Jennifer Hillman Jackson25k

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