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Forum: RNA Sequencing 07-05-2017, 10:49 PM
Replies: 5
Views: 3,106
Posted By nmerienn
Thank you for your advice. I will align them on...

Thank you for your advice. I will align them on rRNA sequences to check if this is remaining rRNA.

But in general, I think there is always some multi-mapped reads in RNAseq data. What is the...
Forum: RNA Sequencing 07-05-2017, 07:40 AM
Replies: 5
Views: 3,106
Posted By nmerienn
Thank you for your answer. Libraries were...

Thank you for your answer.

Libraries were subjected to polyA selection, so there should not be so much remaining rRNA inside (normally).
Forum: RNA Sequencing 07-05-2017, 05:13 AM
Replies: 5
Views: 3,106
Posted By nmerienn
Multi-mapped reads in RNAseq experiment

Dear all,

I am currently working with RNAseq data obtained from different strains of Plasmodium parasite. We are mainly interested in differential expression between the strains. After quality...
Forum: Bioinformatics 05-20-2015, 12:24 AM
Replies: 5
Views: 5,203
Posted By nmerienn
Hi Bjr÷n, Thank you for your answer, it is...

Hi Bjr÷n,

Thank you for your answer, it is more clear for me now. So I kept both reads for my analysis and it seems to work well.

Best,
Nico
Forum: Bioinformatics 05-15-2015, 09:09 PM
Replies: 5
Views: 5,203
Posted By nmerienn
Hi dpryan, Thank you for your answer. So, if...

Hi dpryan,

Thank you for your answer. So, if I understand well, if both reads are crossing the full sequenced fragment length, then the reverse has no more informations and I can discard it. But...
Forum: Bioinformatics 05-15-2015, 08:05 AM
Replies: 5
Views: 5,203
Posted By nmerienn
Paired-end Illumina reads preprocessing with Trimmomatic

Dear all,

I have few questions about the trimming of adapters with Trimmomatic. I have 2x150 bp paired end runs from Illumina MiSeq system. Normally, based on FastQC, there should not be a lot of...
Forum: Illumina/Solexa 05-04-2015, 09:02 AM
Replies: 9
Views: 3,256
Posted By nmerienn
Indeed, this could be an explanation. In our...

Indeed, this could be an explanation. In our case, we are editing the mammalian genome with an adapted CRISPR system (with a targeting on a specific gene). So there is no real CRISPR related genes as...
Forum: Illumina/Solexa 05-02-2015, 02:03 AM
Replies: 9
Views: 3,256
Posted By nmerienn
I found in publications that indels created by...

I found in publications that indels created by the CRISPR system are often small and centered at the cleavage site (majority are less than 10bp). Is it too large to be tolerated by Bowtie 2 of...
Forum: Illumina/Solexa 05-01-2015, 08:12 AM
Replies: 9
Views: 3,256
Posted By nmerienn
Thank you for your help. I will try like this and...

Thank you for your help. I will try like this and come back if I have problems.
Nicolas
Forum: Illumina/Solexa 05-01-2015, 06:56 AM
Replies: 9
Views: 3,256
Posted By nmerienn
Dear Westerman, Thank you for your answer. I...

Dear Westerman,

Thank you for your answer. I was suspected that the answer would not be easy...
If I understand well how pindel and cortex are working, it is doing the same kind of analysis as...
Forum: Illumina/Solexa 04-30-2015, 10:25 AM
Replies: 9
Views: 3,256
Posted By nmerienn
Indels quantifications with MiSeq

Dear all,

I have troubles for analysing CRISPR experiments with sequencing. I am using PCR to amplify the target sequence of my sgRNA (classical PCR product of 400-500 bp) and then use paired-end...
Forum: Bioinformatics 09-12-2014, 01:20 AM
Replies: 92
Views: 36,048
Posted By nmerienn
Gage analysis for RNAseq

Dear all,

We are two biologists (so not bioinformaticians...) working with RNAseq data and having little "troubles" with pathways analysis. We performed RNA sequencing on 4 distinct cell...
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