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Forum: RNA Sequencing 12-13-2016, 09:35 AM
Replies: 0
Views: 962
Posted By mavadhani
Cuffdiff not generating the fpkm values

Hello All,

I am trying to generate a python pipeline to analyze RNASeq data. I am able to build an index of the genome, align the fastq files to the genome and get a sam output and sort the sam...
Forum: General 12-08-2016, 10:14 AM
Replies: 6
Views: 2,270
Posted By mavadhani
That is what I am using. samtools view works...

That is what I am using. samtools view works fine. The sort function works only on bam input, not on the sam input.

I downloaded unix utilities from ...
Forum: General 12-08-2016, 09:20 AM
Replies: 6
Views: 2,270
Posted By mavadhani
Thanks GenoMax. Samtools sort sorts only bam...

Thanks GenoMax. Samtools sort sorts only bam files on the windows 10 terminal. With the sam file input, it gives the following error: samtools.exe has stopped working.

Also, does pysam work...
Forum: General 12-08-2016, 07:03 AM
Replies: 6
Views: 2,270
Posted By mavadhani
Hi wdecoster, Thanks for your response....

Hi wdecoster,

Thanks for your response. Samtools sort function does not work on the windows terminal with either sam or bam files. But the samtools view function converts sam to bam format...
Forum: General 12-07-2016, 08:19 AM
Replies: 6
Views: 2,270
Posted By mavadhani
Help with sorting sam files in python!

Hello All!

I am new to coding. I have written a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess module to call bowtie2 in order to index the genome...
Forum: General 11-10-2016, 06:22 PM
Replies: 2
Views: 1,958
Posted By mavadhani
Thank you very much dpryan. I will certainly...

Thank you very much dpryan. I will certainly give snakemake a shot.

-Madhavi
Forum: General 11-10-2016, 08:59 AM
Replies: 2
Views: 1,958
Posted By mavadhani
Python script for bowtie2 alignment

Hello All!

I am new to coding and am trying to write a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess module to call bowtie2 in order to index the...
Forum: RNA Sequencing 10-05-2016, 09:24 AM
Replies: 0
Views: 759
Posted By mavadhani
Help with genes.gct file on IGV

Hello All!

I am using RNAseq data from a bacterium to identify genes that show differential expression. I used the genepattern platform to align my reads in the fastq files to the genome using...
Forum: Introductions 09-22-2016, 09:49 AM
Replies: 1
Views: 985
Posted By mavadhani
Help with TOPHAT on genepattern

Hello everyone!

I am new to bioinformatics. With a strong background in molecular biology and biochemistry, I am looking to transition to bioinformatics.

I want to look at differential gene...
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