Hi all I am very new in exome seqeucing for SNP variants calling. I got my overall alignment rate of 97.02%. Can Trimmomatic do exome trimming for Hiseq PE? i didnt have information about the sequencing cycle....
Also, from fastqc reports that my per base sequence quality is fine but the "per base sequence content" seems not okay...... http://oi64.tinypic.com/2nbrgjp.jpg
Last question, when i didnt put an index reference (-t) when i piped in my alignment into samtools view .... it looks fine for me so far, does anyone has any experience on this could give some comment to me? Thank you all very much :)
See: How to add images to a Biostars post
Your image address is http://oi64.tinypic.com/2nbrgjp.jpg, not http://tinypic.com/r/2nbrgjp/9
thank you, just change it
Not correctly, read the post again.
Why is your title about assembly?