I have five SRR files for one sample (five runs, Single read - Illumina experiment). What are the steps to be taken before further analysis? I am converting this files to fastq format. Should I merge this five fastq files before mapping to the genome or map them separately. I am new to NGS and don't fully understand what "runs" means. Should I understand them as five independent experiment repeats and analyse separately?
1 answer
Hi Most mappers accept multiple fastq files, so no need of merging them as long as read1 and read2 files are properly supplied. It is also best to retain the original header line of the fastq (-F argument to fastq-dump). See here https://edwards.sdsu.edu/research/fastq-dump/ . The header can be important for FastQC and other downstream applications. SRA classifies as Sample (SRS/ERS) -> Experiment (SRX/ERX) ->Data (SRR/ERR). SRR* files are the resulting data files of a particular experiment (SRX) run on a particular sample (SRP). Running same experiment on the same sample multiple times can result in multiple SRR files.
Log in to answer this question.
-
Multiple SRR files correspond to the same GSM in GEO
written by SHIRUI •
-
Do I need to merge files after downloading them from SRA?
written by bioinfo •
-
Alignng RNAseq data for gene prediction
written by karthic
-
Assembly of oxford nanopore sequencing data
written by MG_19 •
-
NGS analysis: how to handle paired-end reads
written by m98
-
Handling BAM files in technical replicate situations
written by David_emir
-
Trimmomatic: Does it matter to trim the fastq before or after merging multiple replicates?
written by tunl
-
Difficulty in understanding the experimental design ofa RNASeq project
written by nazaninhoseinkhan
-
realignment of TCGA mirna-sequencing
written by biobiu
-
Gatk Variant Discovery And Filtering Process For 500K Target Regions
written by Nino •
