How to merge the pair end sample for GBS analysis in TASSEL software?

Dear sir/Madam

I am very new to GBS (genotype by sequencing) analysis, I have completed one test run for pair-end read samples, the output of the hapmap.txt text file is shown below figure,

each sample has two files in the hmp.txt for example S188_R1.clean.fq.gz, S188_R2.clean.fq.gz please advise me Is this analysis meaningful?, or else I have merged the paired sample in a single file and then run GBS

enter image description here

gbs plot gappit

• 682 views • link

updated 4.3 years ago by Carlo Yague

• written 4.3 years ago by mathavanbioinfo

0 answers

No answers yet.

More posts like this

Cannot use more than 2 sample IDs when demultiplexing using Demuxlet
written 2.0 years ago by Chilly •

Hi Everyone, I currently have a scRNA-seq BAM file of 6 coral individuals mixed together with the genotype (SNP) of each coral. Coral individuals are …
Deseq2 output and robust PCA (PcaGrid and PcaHubert)
written 2.6 years ago by Emma •

Hello there, I followed the deseq2 file to get the list of differentially expressed genes of a dataset I am working on. The Pca graph …
Kraken2 + Bracken with short reads (~20 bases) as input
written 3.0 years ago by jammydodger123456 •

I have small RNA sequencing data (fastQC read length graph below) from rat tissue across two conditions and would like to investigate the presence of …
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
written 8.9 years ago by Rox

This tutorial addresses to anyone in possession of PacBio sequencing data. After struggling myself to find and test appropriated tools, learning PacBio specific format, asking …
Tutorial: InsideDNA: Analysing raw sequencing reads with FASTQC for quality control and filtering
written 10.2 years ago by shilparaopradeep •

Quality control and filtering of sequencing reads is one of the most important steps in the pre-processing of sequencing reads. However, it is not always …