Friday, September 18, 2015

Computational biologist's lab notebook

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Schnell lab from University of Michigan recently published an interesting editorial in PLOS Comp. Bio. ( article link ).  It covers various...
Monday, August 24, 2015

Another RNA-Seq tool from Lior Pachter's lab: Sleuth

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New RNA-Seq based expression estimation program, sleuth', was released today from Lior Pachter's group. This one  challenges curre...
Wednesday, July 22, 2015

RNA-Seq expression metrics: FPKM, RPKM and TMP explained by StatQuest

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FPKM / RPKM and TPM are one of the most widely used transcript and gene expression normalization methods in RNA-Seq studies. FPKM and RPK...

New ovarian cancer study on large structural variants based on TCGA data is out

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We have recently published a study on ovarian cancer using whole genome sequence (control + tumor), RNA-Seq and microarray gene expression c...
1 comment:
Monday, August 4, 2014

How to filter out background noise from the transcriptome assembly? -- Part 4

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( Previous post in this series ) Hello readers, In this post, I'll discuss yet another method to filter out background noise from th...
Tuesday, July 22, 2014

How to filter out background noise from the transcriptome assembly? -- Part 3

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( Previous post in this series ) ( Next post in this series ) Dear readers, Continuing with the new post in the blog series about...
Sunday, April 27, 2014

How to filter out background noise from the transcriptome assembly? -- Part 2

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( Previous post in this series ) ( Next post in this series ) Dear readers, This post is in continuation of my previous blog post  abo...
Sunday, February 9, 2014

Functional genomics and gene-symbols

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Post- genome/transcriptome analysis, especially in cancer or other disease related study, usually ends up in functional genomics that includ...
3 comments:
Sunday, January 26, 2014

How to filter out background noise from the transcriptome assembly? -- Part 1

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Dear readers, Apologies for not being active on the blog for a while. I have been planning to write on this topic for a long time so her...
2 comments:
Tuesday, November 12, 2013

Difference between Cuffcompare and Cuffmerge

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Cufflinks is one of the most commonly used program for reference-genome based transcriptome assembly, and expression estimation and dif...
4 comments:
Wednesday, October 2, 2013

FPKM/RPKM normalization caveat and upper quartile normalization

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FPKM (fragments per kilo bases of exons for per million mapped reads) or RPKM ( fragments per kilo bases of exons for per million mapped r...
3 comments:
Sunday, September 29, 2013

How much memory does TopHat require?

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I've been using Tophat  program for aligning the RNA-Sequencing reads to the reference genome. I mainly run my jobs on computing clust...
Friday, April 5, 2013

How to parse compressed text files using Perl

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Large data files such as FASTQ files from sequencing runs may reach up to gigabytes in size and they can fill up system's disk easily a...
17 comments:
Monday, April 1, 2013

Picard "no space left on device" error

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Sometimes Picard's tools terminate with the error message  "no space left on device" even though there is plenty of space ava...
Sunday, March 31, 2013

Why short-read alignments are always not reproducible?

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Some of you may have noticed that if you re-run a short-read aligner (such as BWA or SOAP) on the same data multiple times then the report...
Monday, February 4, 2013

How to improve RNA-Seq alignment using TopHat

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Hello readers, TopHat is the program to align RNA-Sequencing reads to the reference genome. TopHat is a spliced-read aligner that aligns r...
27 comments: