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SNP calling in Identical exons of two different genes

identical exon snp alignment homolog genome written 5 months ago by Sudhir Jadhao • 60

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Recent Replies

C: edgeR DGElist Error: Negative counts not allowed. by ma23 • 10
The output of **DGEList(count=data.matrix(countDF))**: Repeated column names found in count ...
C: Ideas on how to evaluate genomic coordinates remapping tools? by juliette • 20
Oh I see, thank you for explaining. It is an interesting idea, however I only have the variant co...
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Thanks for reply !!. But I need to download all the bacterial genomes from RefSeq/Genbank and i...
C: Ideas on how to evaluate genomic coordinates remapping tools? by juliette • 20
The basic idea is to create "reads" from the flanking sequences of each variant (using the old as...
C: edgeR DGElist Error: Negative counts not allowed. by Kevin Blighe ♦ 46k
...and what happens when you coerce it to a data matrix? DGEList(count=data.matrix(countDF))...
C: edgeR DGElist Error: Negative counts not allowed. by ma23 • 10
'data.frame': 58302 obs. of 20 variables: $ SRR1177686: int 0 32 2 1 0 0 0 0 0...
A: Can I compare TPM values for a transcript across different transcriptome assembl by kristoffer.vittingseerup • 2.0k
I have to say I tend to disagree with JC and Friederike. According to this [blogpost][1] by Harol...
C: How to Fix Error in snpeff by supriyaslsuman97 • 0
When i had run both the commands Nothing was seen in my case.
A: prepDE.py error - line 255 - gene ID related by kristoffer.vittingseerup • 2.0k
I would suggest useing R instead. There you can use tximport (from the [tximport][1] package) or ...
C: Is it possible to use gene count table (.csv) in ballgown package to determine d by kristoffer.vittingseerup • 2.0k
I have to second that Ballgown should not be used. It always performs very poorly in benchmarks (...
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With regards to introns the answer depends on technology. For bulk-RNASeq data intronic reads are...
C: How to quantify gene expression when stringtie considers two adjacent genes as s by kristoffer.vittingseerup • 2.0k
I do not know how to handle transcripts that span both of them - which is the reason why StringTi...

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