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Forum: RNA Sequencing 02-23-2017, 06:18 PM
Replies: 8
Views: 2,779
Posted By rajesh1989
i got the answer. i think this is some issue with...

i got the answer. i think this is some issue with multi threading. when i run tophat on single core i get correct results. other peoples have also reported this issue.
Forum: RNA Sequencing 02-22-2017, 09:44 PM
Replies: 8
Views: 2,779
Posted By rajesh1989
no they are not in very same folder i have those...

no they are not in very same folder i have those two files.
Forum: RNA Sequencing 02-22-2017, 07:21 AM
Replies: 8
Views: 2,779
Posted By rajesh1989
Hello, whatever i have written here is...

Hello,

whatever i have written here is correct i just copied details and pasted here.

what do you mean by mismatched files?

that is my actual query why tophat is taking only ~460k read pairs?
Forum: RNA Sequencing 02-22-2017, 06:21 AM
Replies: 8
Views: 2,779
Posted By rajesh1989
thank you for the reply. this is output of...

thank you for the reply.
this is output of tophat prep_reads.info

left_min_read_len=25
left_max_read_len=101
left_reads_in =6673385
left_reads_out=6667431
right_min_read_len=25...
Forum: RNA Sequencing 02-21-2017, 07:51 PM
Replies: 8
Views: 2,779
Posted By rajesh1989
what is wrong with samtools flagstat or read mapping with tophat?

I have 6,673,385 (around 6 million) reads in each pair end file after quality filtering. but when i map it using tophat and run samtools flagstat on bam file it gives following output
1343686 + 0 in...
Forum: RNA Sequencing 07-08-2016, 10:51 AM
Replies: 1
Views: 982
Posted By rajesh1989
how many replicates are required for discovery of novel isoform using RNA-seq

Hello everyone,

can I use RNA-seq data from 3 tissues each having 3,3,2 biological replicates and NO technical replicates to identify novel transcripts using cufflinks RABT based assembly?

if...
Forum: Bioinformatics 02-02-2015, 07:28 AM
Replies: 0
Views: 921
Posted By rajesh1989
RNA-SEQ based transcription start and end site identification

Hello everyone,

I have to identify transcription start and end sites in a sequenced genome using rna-seq reads.(I was wondering if this is even possible)

I have around 40 samples, for each...
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