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Forum: Bioinformatics 01-23-2019, 12:20 AM
Replies: 1
Views: 1,385
Posted By priya
Lightbulb ChIPSeq sequencing depth for histone modifications

Hi,
We would like to sequence mouse Histone modification (H3K4me3,H3K4me1,H3K27me3,H3K27ac) chip-seq samples using illumina Hiseq2500. Previously we sequenced to depth of 40M reads/sample. And the...
Forum: Bioinformatics 10-06-2016, 06:36 AM
Replies: 0
Views: 1,648
Posted By priya
comparision with Published RNA-seq

Hi,
I have RNA seq data which contain information about mRNA levels of two neuronal types (Eg: type A , type B).
Experiments,library preparation, sequencing and other downstream analysis to obtain...
Forum: Bioinformatics 10-15-2015, 06:54 AM
Replies: 14
Views: 2,459
Posted By priya
@blancha Thanks for bringing into my notice about...

@blancha Thanks for bringing into my notice about the latest version, its just updated yesterday .. (https://www.bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf)
I see there are...
Forum: Bioinformatics 10-15-2015, 04:35 AM
Replies: 14
Views: 2,459
Posted By priya
Good to know about those points! Thanks !

Good to know about those points! Thanks !
Forum: Bioinformatics 10-15-2015, 01:25 AM
Replies: 14
Views: 2,459
Posted By priya
Thanks dpryan and blancha for your suggestions! ...

Thanks dpryan and blancha for your suggestions!

@dpryan is correct, I noticed it when I viewed my bam files in IGV, actually its issue with multiple mapped reads for low raw counts.

@blancha: ...
Forum: Bioinformatics 10-13-2015, 06:32 AM
Replies: 14
Views: 2,459
Posted By priya
Dear blancha, I rerun htseq-count (0.6.1) and...

Dear blancha,
I rerun htseq-count (0.6.1) and cufflinks(version 2.2.1) on my RNA-Seq samples without removing the duplicates. But I see the same results now, without much changes

First 3 values...
Forum: Bioinformatics 10-12-2015, 12:33 AM
Replies: 14
Views: 2,459
Posted By priya
Thanks for the suggestion! As the final output...

Thanks for the suggestion! As the final output tables for htseq and cufflinks are delivered for us by sequencing facility, I am not sure which files they used as input for htseqcount and cufflinks...
Forum: Bioinformatics 10-09-2015, 06:29 AM
Replies: 14
Views: 2,459
Posted By priya
Thanks for your reply! Which version of...

Thanks for your reply!


Which version of Cufflinks are you using?
cufflinks/2.1.1 is used on bam files to calculate the fpkms

Also, what is the total number of uniquely mapped reads for each...
Forum: Bioinformatics 10-09-2015, 05:03 AM
Replies: 14
Views: 2,459
Posted By priya
Question Problems with FPKM values

Hi,

I see problems with the fpkm values calculated by cufflinks program. I dont see correlation between counts and fpkms for some genes.

To be more clear I explain my scenario
I have RNA-SEQ...
Forum: Bioinformatics 05-06-2015, 05:53 AM
Replies: 16
Views: 6,374
Posted By priya
I found answer to my question.. changing the...

I found answer to my question.. changing the bowtie or bwa parameters improved my aligning percentages to 2-5% but still left with lot of unaligned reads..
This paper explains it,...
Forum: Bioinformatics 04-27-2015, 11:47 PM
Replies: 16
Views: 6,374
Posted By priya
I cross-checked with human genome, but only 0.2 %...

I cross-checked with human genome, but only 0.2 % of unaligned reads are aligned to human genome. I dont think its the contamination issue. I have done sanity check..i could not find huge...
Forum: Bioinformatics 04-27-2015, 01:30 AM
Replies: 16
Views: 6,374
Posted By priya
In order to obtain uniquely mapped reads ,...

In order to obtain uniquely mapped reads , discarding the multiple hits.
I am not sure whether I can introduce more mismatches (default chosen was :2 )as i have short read sequences of 40-43 bp
Forum: Bioinformatics 04-27-2015, 01:25 AM
Replies: 16
Views: 6,374
Posted By priya
Hi Richard, Thank you ! I see that the most of...

Hi Richard,
Thank you ! I see that the most of reverse complement of reads matches to mm10. It looks little bit strange at this point?

Also I checked my SAM header, it looks like all the...
Forum: Bioinformatics 04-24-2015, 07:21 AM
Replies: 16
Views: 6,374
Posted By priya
Thank you for suggestions. I tried to look into...

Thank you for suggestions. I tried to look into those unaligned reads. For that, while running bowtie I add an extra parameter --un to save the unaligned reads.

bowtie -t -p 1 -m 1 $index/mm10 -q...
Forum: Bioinformatics 04-24-2015, 06:31 AM
Replies: 16
Views: 6,374
Posted By priya
I checked through FASTQC and there is nothing...

I checked through FASTQC and there is nothing poping in "overrepresented sequences"
Is there any other ways to check if there is any problems with adapter contamination..

The read length is 43...
Forum: Bioinformatics 04-24-2015, 05:51 AM
Replies: 16
Views: 6,374
Posted By priya
Issues with ChipSeq mapping

Hi,
I have ChipSeq data, and I mapped the reads with bowtie aligner using mm10 as reference genome.
Out of 16M reads processed, only 3M reads are uniquely mapped and 11M reads failed to align and...
Forum: Bioinformatics 03-09-2015, 07:14 AM
Replies: 7
Views: 1,429
Posted By priya
Hi amitm, Thanks alot for your clear...

Hi amitm,
Thanks alot for your clear explaination. I will try it out :)
Forum: Bioinformatics 03-09-2015, 04:01 AM
Replies: 7
Views: 1,429
Posted By priya
Hi amitm, Thank you for your reply! Can...

Hi amitm,
Thank you for your reply!

Can you please clarify me how to calculate the genome coverage from sequencing experiment.
For sample read coverage, i can easily check the alignment logs...
Forum: Bioinformatics 03-09-2015, 03:00 AM
Replies: 7
Views: 1,429
Posted By priya
I came across this term in paper describing...

I came across this term in paper describing normalization of chip-seq reads .
For your better understanding , I attached screenshoot of lines from the paper .
Forum: Bioinformatics 03-09-2015, 12:24 AM
Replies: 7
Views: 1,429
Posted By priya
Genome size and corrected genome size

Hi,
I came across this term "corrected genome size" while reading one paper. Is there any difference between genome size and corrected genome size. If yes, then what needs to be corrected for genome...
Forum: Bioinformatics 02-27-2015, 03:57 AM
Replies: 0
Views: 785
Posted By priya
Question Consistent peaks from Histone Chip datasets

Hi,
I have 3 histone-marks Chip-Seq data (H3K27AC,H3K4me3,H3K27me3). Each condition has two biological replicates and 2 controls. I used SICER to call the peaks, and results looks promising .

If...
Forum: Bioinformatics 01-22-2015, 04:24 AM
Replies: 2
Views: 1,303
Posted By priya
Thank you for your suggestions and links. It is...

Thank you for your suggestions and links. It is exactly what I was looking for,
Forum: Bioinformatics 01-21-2015, 04:02 AM
Replies: 2
Views: 1,303
Posted By priya
Question Similar trends from RNA-Seq values

Hi,

I have time-series RNA-Seq data . Both FPKM and counts values are available. Especially for the DE analysis, Counts are transformed to voomed values and all the DE-tests are performed. I...
Forum: Bioinformatics 11-07-2014, 02:14 AM
Replies: 0
Views: 748
Posted By priya
motif conservation

Hi,

I have motifs(10-15 nt length) identified in the chip-peak regions. I would like to check whether the identified motif regions are evolutionary conserved across species.

One way I know is...
Forum: Bioinformatics 11-06-2014, 03:47 AM
Replies: 1
Views: 1,242
Posted By priya
Hi, May I know did you find out the answer to...

Hi,
May I know did you find out the answer to your post. Now I am struggling with the similar question. I have short motifs and would like to check those are conserved across few species. Please...
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