Forum: RNA Sequencing
05-15-2013, 11:31 AM
|
|
Replies: 0
Views: 1,541
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: 1,812
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: 2,662
|
|
Forum: Bioinformatics
01-09-2013, 10:15 PM
|
|
Replies: 2
Views: 2,662
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: 1,264
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: 1,464
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: 2,084
|
|
Forum: Genomic Resequencing
11-30-2012, 12:39 AM
|
|
Replies: 3
Views: 2,084
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: 10,526
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: 43,017
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: 2,582
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: 1,566
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: 1,429
|
