Forum: Bioinformatics
01-23-2019, 01:20 AM
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Replies: 1
Views: 1,709
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...
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Forum: Bioinformatics
10-06-2016, 07:36 AM
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Replies: 0
Views: 1,855
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...
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Forum: Bioinformatics
10-15-2015, 07:54 AM
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Replies: 14
Views: 2,629
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Forum: Bioinformatics
10-15-2015, 05:35 AM
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Replies: 14
Views: 2,629
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Forum: Bioinformatics
10-15-2015, 02:25 AM
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Replies: 14
Views: 2,629
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Forum: Bioinformatics
10-13-2015, 07:32 AM
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Replies: 14
Views: 2,629
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...
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Forum: Bioinformatics
10-12-2015, 01:33 AM
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Replies: 14
Views: 2,629
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...
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Forum: Bioinformatics
10-09-2015, 07:29 AM
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Replies: 14
Views: 2,629
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...
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Forum: Bioinformatics
10-09-2015, 06:03 AM
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Replies: 14
Views: 2,629
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...
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Forum: Bioinformatics
05-06-2015, 06:53 AM
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Replies: 16
Views: 7,081
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Forum: Bioinformatics
04-28-2015, 12:47 AM
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Replies: 16
Views: 7,081
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Forum: Bioinformatics
04-27-2015, 02:30 AM
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Replies: 16
Views: 7,081
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
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Forum: Bioinformatics
04-27-2015, 02:25 AM
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Replies: 16
Views: 7,081
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Forum: Bioinformatics
04-24-2015, 08:21 AM
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Replies: 16
Views: 7,081
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Forum: Bioinformatics
04-24-2015, 07:31 AM
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Replies: 16
Views: 7,081
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...
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Forum: Bioinformatics
04-24-2015, 06:51 AM
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Replies: 16
Views: 7,081
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...
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Forum: Bioinformatics
03-09-2015, 08:14 AM
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Replies: 7
Views: 1,535
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Forum: Bioinformatics
03-09-2015, 05:01 AM
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Replies: 7
Views: 1,535
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...
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Forum: Bioinformatics
03-09-2015, 04:00 AM
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Replies: 7
Views: 1,535
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Forum: Bioinformatics
03-09-2015, 01:24 AM
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Replies: 7
Views: 1,535
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...
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Forum: Bioinformatics
02-27-2015, 04:57 AM
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Replies: 0
Views: 842
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...
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Forum: Bioinformatics
01-22-2015, 05:24 AM
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Replies: 2
Views: 1,370
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Forum: Bioinformatics
01-21-2015, 05:02 AM
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Replies: 2
Views: 1,370
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...
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Forum: Bioinformatics
11-07-2014, 03:14 AM
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Replies: 0
Views: 811
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...
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Forum: Bioinformatics
11-06-2014, 04:47 AM
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Replies: 1
Views: 1,317
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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