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Search: Posts Made By: ozs2006
Forum: Bioinformatics 12-25-2011, 09:33 AM
Replies: 0
Views: 1,987
Posted By ozs2006
RNA-seq reads counting: sum or max

Hi guys,
From first time I entered RNA-seq analysis, I always count the total number of reads that map to certain genomic area (with coverageBed of BEDTools or my own scripts) and then normalize...
Forum: Bioinformatics 11-27-2011, 11:10 AM
Replies: 6
Views: 3,259
Posted By ozs2006
I created the fastq files from the sam files of...

I created the fastq files from the sam files of the publication (using awk) and then ran tophat.

1. awk:

awk '{if($2==99) print "@" $1 "\n" $10 "\n" "+\n" $11}' > sample_1.fq
awk '{if($2==147)...
Forum: Bioinformatics 11-27-2011, 10:40 AM
Replies: 6
Views: 3,259
Posted By ozs2006
Thanks for the quick reply :) As you noted, it...

Thanks for the quick reply :)
As you noted, it is very strange, because all the publicly available reads are flagged as 99 and 147, and I used all of them.
Forum: Bioinformatics 11-27-2011, 07:35 AM
Replies: 6
Views: 3,259
Posted By ozs2006
related question

Hello all,

I understood that in tophat 1.3.3 there is no need to assign the inner distance.
I used data from recent published paper, where all reads in the repository were marked as properly...
Forum: Bioinformatics 10-26-2011, 05:12 AM
Replies: 4
Views: 15,782
Posted By ozs2006
I got similar problem: I downloaded sam...

I got similar problem:

I downloaded sam files from recent published study.
Each sam file contains alignments of the reads to a single chromosome (hg19).
I want to merge alignments into one...
Forum: Bioinformatics 08-10-2011, 11:04 PM
Replies: 2
Views: 2,638
Posted By ozs2006
I'm sorry, Oz

I'm sorry,
Oz
Forum: Bioinformatics 08-10-2011, 01:30 AM
Replies: 2
Views: 2,638
Posted By ozs2006
Smile Visualization of variants from varScan with IGV

Hi all,

I visualized the variant positions I got from varScan using IGV.
I saw that they show different coverage from what I have detected using varScan (usually the IGV have higher coverage for...
Forum: Bioinformatics 07-27-2011, 05:31 AM
Replies: 3
Views: 4,161
Posted By ozs2006
Hi, Does anyone know why varScan detects two...

Hi,

Does anyone know why varScan detects two variants in the same genomic position, same variation but different quality scores?

example:...
Forum: Bioinformatics 06-06-2011, 03:43 AM
Replies: 0
Views: 1,777
Posted By ozs2006
alternative splicig from cuffdiff

I heard Adam Roberts's lecture in Weizmann institute (Israel) yesterday
I have some questions about Alternative splicing analysis from cuffdiff:

1. How to understand intutively the...
Forum: Bioinformatics 04-21-2011, 02:13 AM
Replies: 17
Views: 6,005
Posted By ozs2006
hi, I'm interested using scripture for RNA-seq...

hi,
I'm interested using scripture for RNA-seq analysis of alternative splicing.
Is there a detailed documentation for all the program's flags, (I'm having some trouble making the example at...
Forum: Bioinformatics 02-21-2011, 10:47 AM
Replies: 5
Views: 3,389
Posted By ozs2006
Miso vs. cufflinks

For miso users: What is the feature that distinguish miso from cufflinks, and helped you take miso as your favorite tool?
Forum: Bioinformatics 02-21-2011, 10:41 AM
Replies: 1
Views: 1,901
Posted By ozs2006
I join to your question: Do I need to filter...

I join to your question: Do I need to filter these "bad" flags out, and to trust only the "samtools view -f 2"?
Thanks in advance
Forum: Bioinformatics 12-05-2010, 11:46 PM
Replies: 15
Views: 16,266
Posted By ozs2006
It seems very strange, I ran tophat on other...

It seems very strange, I ran tophat on other lanes of my experiment, and it ran well (more than 50% of properly paired reads according to samtools flagstat). I still don't know why lane 1 running...
Forum: Bioinformatics 11-28-2010, 12:02 AM
Replies: 15
Views: 16,266
Posted By ozs2006
Thanks for your replay :-) I use tophat v1.1.0...

Thanks for your replay :-)
I use tophat v1.1.0 .
Maybe this problem happen because I took the s_1_1_sequence.txt s_1_2_sequence.txt and changed their file extension to s_1_1.fq s_1_2.fq . As...
Forum: Bioinformatics 11-25-2010, 02:34 PM
Replies: 15
Views: 16,266
Posted By ozs2006
The command I used: tophat -r 83 -p 8...

The command I used:
tophat -r 83 -p 8 --solexa1.3-quals /path_to_bowtie_index/bowtie-0.12.5/indexes/h_sapiens_hg18 s_1_1.fq s_1_2.fq

I have paired-end reads with 76 cycles for each side.

1....
Forum: Bioinformatics 11-23-2010, 11:30 PM
Replies: 15
Views: 16,266
Posted By ozs2006
Thanks for the quick reply. 1. here is...

Thanks for the quick reply.

1. here is samtools flagstat output:

23722180 in total
0 QC failure
0 duplicates
23722180 mapped (100.00%)
23722180 paired in sequencing
11861090 read1
Forum: Bioinformatics 11-23-2010, 03:47 PM
Replies: 15
Views: 16,266
Posted By ozs2006
Tophat insert size of paired-end reads

I used tophat to align paired-end 76bp RNA-seq.
The fragments selected at 300bp.
As the example in tophat manual shows- I used: tophat -r 148 ...
When I inspected the .bam with:
samtools view...
Forum: Bioinformatics 10-27-2010, 07:31 AM
Replies: 9
Views: 7,782
Posted By ozs2006
Thumbs up I eventually downloaded samtools 1.0.7a and...

I eventually downloaded samtools 1.0.7a and followed your instructions, then I downloaded binary of tophat.
It work (as it seems from running the test_data) :) .
thank you very much
Forum: Bioinformatics 10-26-2010, 01:01 AM
Replies: 9
Views: 7,782
Posted By ozs2006
Question Diffculty in installing topHat/Cufflinks

Cufflinks and topHat are wonderful softwares, I can't wait to use them on my RNA-seq analysis.
I tried to install topHat from source code.
I followed your instructions, and also install samtools...
Forum: Literature Watch 06-03-2010, 08:41 AM
Replies: 5
Views: 6,921
Posted By ozs2006
that sounds incredible :)

that sounds incredible :)
Forum: Introductions 05-31-2010, 05:53 AM
Replies: 0
Views: 862
Posted By ozs2006
hello everyone

it seems a lovely foruom :)
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