User: nand

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nand10
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Posts by nand

<prev • 6 results • page 1 of 1 • next >
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Comment: C: StringTie inconsistent expression value
... I loaded BAM and merged GTF to IGV. I am seeing many fragments aligned to that transcript region. But FPKM is absolutely zero. ...
written 3 months ago by nand10
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StringTie inconsistent expression value
... I'm trying to find novel isoforms from RNA-Seq. I have six samples, 3 control and 3 treatment. I made a merged gtf file after running StringTie with gencode annotation. Then the merged annotation was used to estimate FPKM in all samples. Then novel transcripts expression was tabulated as shown below ...
rna-seq written 3 months ago by nand10 • updated 3 months ago by genomax49k
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Comment: C: DAVID Fisher Exact Test contingency table
... It still shows the same contingency table. ...
written 4 months ago by nand10
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cuffdiff long noncoding annotation vs full annotation
... I'm studying differential expression of long non coding RNA. Should I run cuffdiff using the gencode annotation file with all transcripts, and then filter out lncRNA data, or run cuffdiff with annotation of only long noncoding RNAs? If I use full transcripts annotation, FPKM values are much lower th ...
rna-seq written 5 months ago by nand10 • updated 5 months ago by Ben50
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Cufflinks shows novel and abundant transcript
... I ran cufflink with **-g** option using gencode annotion file **gencode.vM15.chr_patch_hapl_scaff.annotation.gtf**. I sorted *the **isoforms.fpkm_tracking** based on fpkm and found that there many CUFF.XXX transcripts that have very high FPKM. The deep sequencing data corresponds to a paper publish ...
rna-seq written 5 months ago by nand10 • updated 5 months ago by genomax49k
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cuffdiff between polyA enriched sample and rRNA depleted sample
... Hi, My lab did RNA seq of some samples with just rRNA depletion. Now, there is some RNA-Seq data on GEO that is sequenced after polyA enrichment. Is it possible to cuffdiff my data with the GEO data. At least, is it possible to see differential expression of a list of about 100 transcripts(having ...
rna-seq written 6 months ago by nand10 • updated 6 months ago by WouterDeCoster29k

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