I want to analyze a chip-seq data set in GEO (GSE11431), and I have two questions:
Its SRA file in each of GSM have multiple files/"runs", what does it mean? is it replicates or what? Do I just download all of them and run bowtie individually using same reference genome, and then combine them afterward?
Another question is where can I download mouse reference gene (mm9 version) for bowtie?
Thank you very much for any idea and help!!
1 answer
each time the sequencer is operated to sequence a set of samples is called a "run". So, some samples will be sequenced in multiple "runs", which can be treated as technical replicates. The samples that are sequenced in multiple "runs" will be merged at some point in the analysis pipeline.
There are pre built indexes for bowtie and bowtie2 on their website. http://bowtie-bio.sourceforge.net/index.shtml
If you are looking for annotations as well, tophat website provides a set of genomes and annotations, but the file size will be huge (14-20g).
•
written
by
GouthamAtla
You can merge the raw fastq files before performing any analysis or you can merge the bam files after alignment. It depends on the type of analysis you are doing. Merging after alignment would be good as you can compare the differences between multiple runs after alignment and then merge.
Log in to answer this question.
-
How to proceed with multiple runs ChIP-seq
written by buffealo •
-
how to aligned to mouse pre-rRNA
written by 17318598206 •
-
Mapping multiple SRR ID from same experiment
written by singlecell •
-
Problem with downloading GSE file by GEOquery
written by Kim •
-
rsem-prepare-reference and mouse mm9 genome reference files
written by moxu
-
SRA/ GEO format help
written by datanerd
-
ChIP-Seq contaminated by human tissue?
written by Gary
-
normalize on chip-seq data
written by catherine
-
visualize tiling array file to IGB
written by catherine
-
how to treat replicates with Chip-seq meta-analysis
written by Krisr
