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Search: Posts Made By: Rangika
Forum: Bioinformatics 09-28-2016, 07:57 PM
Replies: 0
Views: 1,792
Posted By Rangika
Question Low coverage after alignment

Hi,

I'm working with a illumina Miseq 2*300bp PE 8 sample library run on a single lane of a flowcell. Ref ~32Mbp in size. I aligned PE raw dataset for one sample against the reference sequence...
Forum: Bioinformatics 09-20-2016, 08:29 PM
Replies: 4
Views: 1,565
Posted By Rangika
Thank you Michael for your answer. Regards ...

Thank you Michael for your answer.

Regards
Sumudu
Forum: Bioinformatics 09-20-2016, 01:14 AM
Replies: 4
Views: 1,565
Posted By Rangika
Thank you Michael. My dataset is DNA-seq. Can I...

Thank you Michael. My dataset is DNA-seq. Can I use RSeQC tools to check alignment for DNA data as well. Do you suggest RSeQC statistics would lead in to better BAM selection?

Appreciate if you...
Forum: Bioinformatics 09-19-2016, 08:37 PM
Replies: 4
Views: 1,565
Posted By Rangika
Question Selecting the best alignment BAM file

Hi,

I have a PE dataset 300bp inserts by illumina MiSeq. I aligned the raw data using BWA-mem. Mapping statistics generated using Samtools flagstat are below.

5541008 + 0 in total (QC-passed...
Forum: Bioinformatics 09-09-2016, 06:30 PM
Replies: 2
Views: 3,415
Posted By Rangika
Thank you Brian. I will proceed & see as you have...

Thank you Brian. I will proceed & see as you have suggested.
Forum: Bioinformatics 09-08-2016, 10:01 PM
Replies: 2
Views: 3,415
Posted By Rangika
Quality trimming & filtering illumina reads

Hi,

I have a illumina MiSeq data set, 32GB size genome, 300bp reads. Quality of reads degrades towards the 3' end in both R1 & R2, more in R2. I want to align reads to its reference using BWA-mem...
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