I'm totally new to bioinformatics and using linux. So, I've run a 'read until' targeting on several genes and these are the steps that I've been taking:
1) porechop the fastq file 2) nanofilt it to exclude reads which are > 50k b.p 3) use minimap to align it to hg38 and sort it at the same time 4) Index the bamfile 5) load into IGV.
I couldn't see a thing. So, referring to old posts, that someone facing the same issue. It is recommended to pull up the header to see what's the first few output.
I use this script:
samtools view -h bamfile | head -30
It gave me a whole list of this:
@HD VN:1.3 SO:coordinate @SQ SN:chr1 LN: 248956422
I can't see any indicators on which chromosome should i focus on in IGV...this makes me wonder did one of the steps gone wrong?
Your help is much appreciated. Thank you.