Single read analysis needed

1

I have been sequencing a human whole exome run using Illumina Nextseq 550, the read1 was in good quality and read2 totally failed. my question is
Can I analyze the only read1 and exclude read2 and how?

2

Hi @ahmed_saeed
yes, you can map forward reads only. During setup of mapping job select Single if you use BWA-MEM. The default type of data in Bowtie2 is Single-end, so no need to change anything. I assume you have two FASTQ.gz files, one with F and another with R reads.
Kind regards,
Igor

3

Thanks @igor Yes i have two Fastq files, How can I analyze my data from F read only?

4

Hi @ahmed_saeed
I am sorry for unclear description. If you use bowtie2, just select file with F reads, and choose an appropriate reference genome. If you use BWA-MEM, change type of data to Single, select F file, and provide an appropriate reference genome.
Hope it does make sense.
Kind regards,
Igor