User: yasokannan93

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yasokannan9320
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Posts by yasokannan93

<prev • 5 results • page 1 of 1 • next >
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Noncode transcripts with strand information as .
... Hi, I am trying to work with annotations from [noncode][1] and have downloaded the http://www.noncode.org/datadownload/NONCODEv5_human_hg38_lncRNA.gtf.gz gtf file. While processing the file, I noticed some of the transcripts have . (dot) as strand. I was wondering why this is occurring. eg: NONHSA ...
lncrna written 3 days ago by yasokannan9320
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Answer: A: TCGA dataset has 2 HTSeq readcounts file for same tisssue
... A similar post: https://www.biostars.org/p/308192/ Based on the approach here, you can use aliquot with later plate number. You will have to get the full TCGA barcode for this sample and choose one. To know about the TCGA codes: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ https:/ ...
written 6 days ago by yasokannan9320
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Comment: C: How to get an exact match from the bam alignment file
... Thanks for the clarification. So for the example, we should expect it as MD:Z:100 ? https://samtools.github.io/hts-specs/SAMtags.pdf says > The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means from the leftmost reference base in ...
written 25 days ago by yasokannan9320
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Answer: A: How to get an exact match from the bam alignment file
... You can use a combination of read length and the cigar character M from the alignment file. For example, if the read length is 100, you can try extracting reads with cigar score of 100M. This would mean the read is completely consistent or it is an exact match. ...
written 25 days ago by yasokannan9320
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Answer: A: how i can use SRA accession Number to call raw reads ?
... Both the options (FASTQ files FTP and NCBI SRA file FTP) can be used. Its the same file. ...
written 5 weeks ago by yasokannan9320

Latest awards to yasokannan93

Scholar 6 days ago, created an answer that has been accepted. For A: TCGA dataset has 2 HTSeq readcounts file for same tisssue

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