User: Sameet

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Sameet290
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5 years, 3 months ago
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Posts by Sameet

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Transcription Factor Dna-Binding Sites
... Genomatix is a paid data-base that has this information. I believe there is a program called Match. The link provided points to a page that has the information about many programs. You need to register, and you can use the "free" version of the program on the website. If you need to do anything m ...
written 5.4 years ago by Sameet290
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Comment: C: Hic Analysis Tools Comprehensive List
... Yes, I have used HiTC extensively, and the author is very helpful. But the package only comes into play after you have aligned the data, and processed the interaction matrix. There is nothing in HiTC that will help you align the data. ...
written 5.4 years ago by Sameet290
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Answer: A: How To Calculate The Sample Sizes Need To Discover Motifs
... There is a slight problem with your approach. If you want a motif that is potentially present in all the sequences, then this method may not work very well. There is only a slight chance it will work at all actually. I would draw at least 50% of the sequences randomly, determine a motif, and repe ...
written 5.4 years ago by Sameet290
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Hic Analysis Tools Comprehensive List
... Has anybody compiled a list of tools available for HiC analysis? I know about the Mirnylib, the Homer, and the HiC Inspector. But I am not aware of many other tools. I want to know what other tools exist that I an use to analyze HiC data. By Analysis I mean from the fastq.gz files to the intera ...
written 5.4 years ago by Sameet290 • updated 4.5 years ago by flyamer30
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Comment: C: Doubts Regarding Calculation Of Fpkm Values By Cuffdiff?
... I think i was not clear. My situation is as follows. I have 3 bam files, a.bam, b.bam, and c.bam. I have a single annotation file, annotation.gtf. If i use this annotation file with a.bam, and b.bam, I get a set of FPKM values, but if i now use a.bam, and c.bam with same annotation file, and sam ...
written 5.7 years ago by Sameet290
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Doubts Regarding Calculation Of Fpkm Values By Cuffdiff?
... Hi, Recently we sequenced a bunch of RNA Seq libraries. I wanted to compare the gene expression levels between all of them. So I used the standard annotation gtf file with the tophat aligned bam file with cuffdiff. I extract the FPKM matrix using cummeRbund. What has me confused is depending on ...
rnaseq analysis cuffdiff written 5.7 years ago by Sameet290 • updated 5.7 years ago by Nick260
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What Do The Columns Of "Junctions.Bed" File Mean?
... Hi, I have seen the junctions.bed file created everytime I run tophat. I tried reading through the manual, but I could not find a satisfactory explanation for all of the columns in this file. Is there any resource where this description is available in detail. ...
tophat bam written 5.8 years ago by Sameet290 • updated 5.8 years ago by cpcantalapiedra140
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Comment: C: A Question About Samtools And Calculating Depth
... Thank you @ashutoshmits. This was very helpful. ...
written 6.2 years ago by Sameet290
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Comment: C: A Question About Samtools And Calculating Depth
... I do have the cufflinks output for these. But i only wanted to see if i can visualize the alignment itself. ...
written 6.2 years ago by Sameet290
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A Question About Samtools And Calculating Depth
... I have some RNA-Seq data. I want to know if there is a way to use samtools to calculate strand-specific depth from the accepted_hits.bam file generated by tophat. ...
depth-of-coverage samtools written 6.2 years ago by Sameet290 • updated 6.2 years ago by Ashutosh Pandey11k

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