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Search: Posts Made By: aquleaf
Forum: Epigenetics 03-07-2016, 09:20 PM
Replies: 0
Views: 1,297
Posted By aquleaf
Insert size range in ChIP-Seq

Hi All. May I ask a question regarding ChIP-Seq library preparation?

The input looks good with summit at ~200bp according to Bioanalyzer. However, the size distribution of ChIPed DNA shift with...
Forum: Bioinformatics 03-03-2016, 07:23 AM
Replies: 1
Views: 733
Posted By aquleaf
experimental design of ChIP-Seq

Hi all. I have a question regarding the experimental design of ChIP-Seq. We have cells in two different states, and we would like to compare the binding profile differences between two states. Should...
Forum: Epigenetics 03-03-2016, 07:15 AM
Replies: 0
Views: 2,074
Posted By aquleaf
Questions regarding ChIP sonication and ChIP-Seq on heterochromatin

Hi all. I have a problem regarding ChIP sonication. We are culturing one type of cells in two different states. One state shows active transcription (say State A), while the other one shows decreased...
Forum: Epigenetics 08-18-2015, 08:32 AM
Replies: 1
Views: 1,862
Posted By aquleaf
Is it necessary to perform paired-end sequencing for ChIP-Seq

Hi all. I'm trying to do ChIP-Seq in two different fragmentation ways including sonication and MNase treatment, respectively. I'm wondering is it necessary to perform paired-end sequencing for...
Forum: Bioinformatics 03-02-2013, 03:13 PM
Replies: 5
Views: 1,655
Posted By aquleaf
Thanks very much for your reply. How do you mask...

Thanks very much for your reply. How do you mask them? Is there any software to mask them?

We will also combine the ChIP-Seq data with mRNA-Seq data later on. What's the problem if the duplicates...
Forum: Bioinformatics 03-01-2013, 04:15 PM
Replies: 5
Views: 1,655
Posted By aquleaf
Thanks very much for your reply. We don't want to...

Thanks very much for your reply. We don't want to distinguish which locus these reads come from for a gene with several copies in the genome, we wish to count all the reads uniquely mapped to this...
Forum: Bioinformatics 03-01-2013, 02:10 PM
Replies: 5
Views: 1,655
Posted By aquleaf
Unhappy a Question about Duplicated Genes

Hi all.

I have a question about duplicated genes which have several copies in the genome such as Ccl21c. Tophat was used to map the RNA-Seq reads back to the genome and HTSeq was used to count...
Forum: RNA Sequencing 01-17-2013, 08:29 AM
Replies: 0
Views: 993
Posted By aquleaf
Does Tophat remove the reads falling outside known gene regions

Hi All.

I have a question about Tophat. I mapped the RNA-Seq by both Tophat and Bowtie. When running Tophat, a GTF file of gene annotations was provided. I found some reads were mapped by Bowtie...
Forum: Bioinformatics 01-07-2013, 02:12 PM
Replies: 1
Views: 1,210
Posted By aquleaf
Does Tophat remove duplicates

Hi all.

May I ask a question about Tophat? Does Tophat remove duplicates? Duplicates here mean the reads were mapped to the same genomic region, say, for single end sequencing, the leftmost of...
Forum: Bioinformatics 11-13-2012, 07:30 PM
Replies: 3
Views: 1,921
Posted By aquleaf
Yes, I increase --max-bundle-frags in cuffdiff...

Yes, I increase --max-bundle-frags in cuffdiff step, but still got HIDATA
Forum: Bioinformatics 11-13-2012, 04:32 PM
Replies: 3
Views: 1,921
Posted By aquleaf
HIDATA in Cuffdiff

Hi all. Sorry to bother you.

I have a question about Cufflinks suite. Basically, I used Cufflinks to assemble transcripts and genes, then Cuffmerge to merge all the assemblies and generate an...
Forum: RNA Sequencing 10-30-2012, 08:49 AM
Replies: 5
Views: 4,648
Posted By aquleaf
Thanks for your reply. I agree with you....

Thanks for your reply. I agree with you. Especially our data are single reading, it is difficult to mark PCR duplicates.
Forum: RNA Sequencing 10-30-2012, 08:42 AM
Replies: 5
Views: 4,648
Posted By aquleaf
Thanks for your reply. According to Illumina...

Thanks for your reply.

According to Illumina manual, 15 cycle PCR is performed. So there are about 30,000 copies for each fragment. How could the PCR duplicate level be so low? I guess only a...
Forum: RNA Sequencing 10-29-2012, 07:46 PM
Replies: 5
Views: 4,648
Posted By aquleaf
Unhappy PCR duplicates

Hi all. Sorry to bother you. After reading several threads about PCR duplicates, I'm totally confused.

The last step of library preparation in illumina RNA-Seq is PCR which means a fragment will...
Forum: Bioinformatics 10-26-2012, 02:23 PM
Replies: 1
Views: 1,631
Posted By aquleaf
Distinguish real duplicates from those generated by PCR

Hi All.

Sorry to bother you. Is there a way to distinguish duplicates caused by high sequencing depth from the PCR artefacts?

One more question. Is it necessary to remove the duplicates in the...
Forum: RNA Sequencing 10-25-2012, 10:35 AM
Replies: 0
Views: 934
Posted By aquleaf
Cufflinks HIDATA

Hi All. Sorry to bother you.

I'm wondering why when many fragments are aligned to a locus, cufflinks will skipped and mark it as HIDATA.

Thanks very much!


Best, Mei
Forum: RNA Sequencing 10-16-2012, 02:22 PM
Replies: 3
Views: 1,184
Posted By aquleaf
Read dupliation in RNA-Seq

Hi All.

I have a question about read duplication. Our studied tissue is kind of special. Most of mRNA encode a small number of proteins. So in the FASTQC result, we got a high duplication level (>...
Forum: Bioinformatics 10-03-2012, 07:31 AM
Replies: 0
Views: 792
Posted By aquleaf
Red face segmentation fault with cisGenome

Hi All.

I'm trying to use cisGenome to analyze affymerix ChIP-on-chip data. When importing data by tilemap_importaffy, an error occurs: Segmentation fault. Does anyone happen to have the same...
Forum: Bioinformatics 09-25-2012, 07:54 AM
Replies: 1
Views: 1,825
Posted By aquleaf
Unhappy How to analyze RNA-Seq with 3' bias

Hi All.

I'm trying to identify differentially expressed genes between 2 groups. However, here is the problem. My RNA-Seqs are lack of 5' alignments. I manually checked several genes which were...
Forum: Illumina/Solexa 09-19-2012, 08:01 AM
Replies: 1
Views: 964
Posted By aquleaf
Unhappy a problem with RNA-Seq

Hi All.

I have problems with RNA-Seq. We used TruSeq kit to prepare libraries and Tophat to align reads. Take the following two genes as examples to show our problems.

1712
Almost no reads...
Forum: Bioinformatics 08-08-2012, 08:30 AM
Replies: 1
Views: 965
Posted By aquleaf
Questions about Cuffmerge and Cuffdiff

Hi all.

I have two questions about Cuffmerge and Cuffidiff.

1, Is the merged gtf file generated by Cuffmerge 0-based or 1-based?

2, How to understand more than one reference genes are...
Forum: Bioinformatics 05-08-2012, 09:06 AM
Replies: 1
Views: 1,379
Posted By aquleaf
Unhappy ChIP-Seq mapping rate

Hi.

We performed 36bp ChIP-Seqs in mouse and ran Bowtie to align the reads. Around 50% reads were not mapped. Is it reasonable? Does it mean our ChIP-Seqs were not successful?

Wish your help!...
Forum: Bioinformatics 11-30-2011, 12:53 PM
Replies: 3
Views: 1,334
Posted By aquleaf
Question ChIP-Seq Integration & Interpretation

Hi. I have three ChIP-Seq data for the same sample. Peak calling was done separately. How to combine the peaks of these three experiments together?

One more question, How to associate genes with...
Forum: Bioinformatics 11-30-2011, 12:25 PM
Replies: 1
Views: 1,465
Posted By aquleaf
Try GTF file from Ensemble

Try GTF file from Ensemble
Forum: Bioinformatics 11-05-2011, 06:41 AM
Replies: 2
Views: 2,586
Posted By aquleaf
Unhappy Empty sequence dictionary

Hi.

When I used picardtools ValidateSamFile, it reported the empty sequence dictionary error in sam file. What does this error mean?

Wish help! Thanks very much in advance!
Showing results 1 to 25 of 38

 


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