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Forum: RNA Sequencing 05-15-2013, 11:31 AM
Replies: 0
Views: 1,486
Posted By abh
novoalign mapping

Hi,
I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads

I am new to novoalign(went through the manual) and confused with some of the options like...
Forum: Bioinformatics 04-08-2013, 11:34 AM
Replies: 2
Views: 1,774
Posted By abh
cufflinks multiple FPKM values for same location

Hi,

i have run cufflinks for my Bam files to look after the FPKM values and i got the output.

later i took the output transcripts.gtf and converted into bedgraph file to view in UCSC genome...
Forum: Bioinformatics 01-10-2013, 12:22 AM
Replies: 2
Views: 2,588
Posted By abh
i need to develop a heatmap to compare my chipseq...

i need to develop a heatmap to compare my chipseq data with the encode tss data

for example like the image on the top of this page

http://www.pnas.org/content/107/50/21931/F2.large.jpg

i...
Forum: Bioinformatics 01-09-2013, 10:15 PM
Replies: 2
Views: 2,588
Posted By abh
TSS for encode data

HI,

i am new to chip-seq data analysis and right now i need to develop heatmaps to compare my data with the histone encode data (H3K4me3 and K27me3)

where do i get the TSS annotation files to...
Forum: Bioinformatics 12-05-2012, 05:15 PM
Replies: 0
Views: 1,228
Posted By abh
bigwig file help in UCSC

hi,

i have a bigwig file in my desktop that i need to visualize in UCSC genome browser

can anyone tell me how to move a file to http location and give in the custom track

for example
...
Forum: Genomic Resequencing 12-02-2012, 04:41 PM
Replies: 0
Views: 1,420
Posted By abh
Tophat RnaSeq(20-36bp)bp reads

Hi,

I have 2 RnaSeq fq files that i need to analyze.i did the quality trimming and adapter trimming for the files as they were need to do it

then i got 2 output files that are 1.fq file(36...
Forum: Genomic Resequencing 11-30-2012, 10:06 AM
Replies: 3
Views: 2,022
Posted By abh
thank you Its working now

thank you

Its working now
Forum: Genomic Resequencing 11-30-2012, 12:39 AM
Replies: 3
Views: 2,022
Posted By abh
Tophat with bowtie2

Hi,

I want to align the Rna-seq data using bowtie2.so here are the steps i did(i installed tophat,bowtie2 and samtools and kept in bashprofile)

i got the reference genome from bowtie2(hg19) and...
Forum: Bioinformatics 11-21-2012, 10:06 AM
Replies: 1
Views: 10,365
Posted By abh
open Html file and png file in unix

hi

I ran fastqc on the fastq files and i got output in a folder which contains html files and png files in it
how do i open them within the unix command line?

I tried using firefox and...
Forum: RNA Sequencing 11-08-2012, 11:23 AM
Replies: 2
Views: 42,956
Posted By abh
De-Multiplexing MiSeq Data

Hi,

I have 3 fastq files consisting of R1, R2 read files and
a separate index file. for example They are in the format below.

R1: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
Sequence...
Forum: RNA Sequencing 11-07-2012, 08:27 PM
Replies: 0
Views: 2,490
Posted By abh
demultiplexing fastq data(RNA-Seq data)

Hi,

I have 3 fastq files consisting of R1, R2 read files and
a separate index file. for example They are in the format below.

R1: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
Sequence...
Forum: Bioinformatics 11-07-2012, 08:10 PM
Replies: 0
Views: 1,493
Posted By abh
demultiplexing fastq data(RNA-Seq data)

HI,

I have three fastq files one is the index file with barcodes and two paired end read files.i need help in performing demultiplexing of index file(fastq file) by taking the barcode and search...
Forum: Introductions 08-08-2012, 10:54 AM
Replies: 0
Views: 1,375
Posted By abh
need help in R programming

R programming help in recode genotypes for snp data
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