User: qudrat

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qudrat20
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NATIONAL INSTITUTE OF IMMUNOLOGY, INDIA
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q*****@nii.ac.in

Can somebody tell me how mask gtf file is generated?

Posts by qudrat

<prev • 36 results • page 1 of 4 • next >
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Comment: C: cuffcompare and cuffmerge
... But in case of option #3 some transcripts might be missed because I have tried both strategy and in option #2 i.e Cuffcompare have more number of transcripts. In Cuffmerge I think there is a chance of getting false positive. ...
written 7 days ago by qudrat20
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Comment: A: cuffcompare and cuffmerge
... Thank you very much Kevin Blighe! ...
written 7 days ago by qudrat20
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Comment: C: Getting the number of Genes expressed in a sample
... If you have done Cufflinks you could see genes.fpkm_tracking file to count the number of gene and isoforms.fpkm_tracking file to see total number of transcripts ...
written 7 days ago by qudrat20
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cuffcompare and cuffmerge
... When we merge two GTF file from two different sample, Is it true that Cuffcmerge lists common transcripts between two sample and Cuffcompare produce all the transcripts between two sample with no redundancy? ...
next-gen rna-seq written 7 days ago by qudrat20
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cuffcompare and cuffmerge
... Hi folks, To find novel transcript in an organism via RNA-Seq, some use Cuffcompare to merge different gtf files produced from Cufflinks while some use Cuffmerge for the same. Please help me to get over this. Thank you ...
next-gen rna-seq written 8 days ago by qudrat20
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Stringtie and Cufflinks and Cuffmerge
... Can Cuffmerge be used to merge different gtf files produced from Stringtie as I have fourteen gtf files from Stringtie ...
assembly rna-seq written 10 days ago by qudrat20 • updated 10 days ago by kristoffer.vittingseerup300
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Comment: C: FPKM threshold and filter
... My real aim is to find novel genes and many genes show very less value of FPKM. ...
written 10 days ago by qudrat20
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FPKM threshold and filter
... Can somebody suggest me how to choose the minimum FPKM value as a threshold to filter low quality transcripts? ...
next-gen rna-seq written 11 days ago by qudrat20 • updated 10 days ago by igor4.6k
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HISAT2 analysis and transcriptome assembly
... Can I produce human genome index file for HISAT2 if I have a computer with only 16GB RAM? Please somebody suggest me or whether can it be downloaded? ...
assembly rna-seq written 13 days ago by qudrat20 • updated 13 days ago by Vijay Lakhujani1.3k
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Comment: C: read coverage and transcripts
... Yes I want to assess the coverage in alignment. Actually in my question, I wanted to make it clear that what software I used ...
written 16 days ago by qudrat20

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