Chip_seq analysis remove duplicates
Hello everyone I am analyzing Chip-seq data. In fragmentation step we used Micrococcal Nuclease in this condition can I remove duplicate reads from bam file after mapping or not can anyone suggest me. Read many related papers some people are removing duplicates and some are not confused what to do. PCR showing bands 150, 300, 450, 600 etc. is this fragmentation size matters in chip-seq because more than 1k bands are visible as its almost cutting around random nuleosome position. I need some expert opinion.
Thank you
• 1,180 views
•
link
written
by
luckysardar171 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
written by txema.heredia •
-
Blog: Next generation sequencing and its clinical applications
written by Novogene •
-
Exact duplicated reads between independent replicates
written by Miguel •
-
What could be the cause of different levels of binding in ChIP-Seq Input samples?
written by Aspire
-
If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
written by salamandra
-
Alternate allele bias in RNA-seq data?!?!?!
written by mdgallagher71 •
-
Tutorial: Guide to TCGA data
written by Jordan Anaya
-
handling PCR duplicate reads ?
written by GouthamAtla
-
News: Bioinformatics Hands-On Workshop: Discovering standard and non-standard RNA transcripts
written by David Langenberger
-
Best Way To Preprocess Barcoded Illumina Paired-End Data
written by Ying W
For MNase ChIP-seq I would avoid removing PCR duplicates unless you have UMIs on your adapters. Fragment ends are expected to be more uniform since you are chewing unbound DNA away instead of fragmenting in a semi-stochastic manner.
Okay, thank you for the reply, My fragment size varying lot does it matters in chip-seq