I am completely new to this, any help will be greatly appreciated.
After running hisat2, I get
“Error, fewer reads in file specified with -1 than in file specified with -2 libc++abi.dylib: terminating with uncaught exception of type int (ERR): hisat2-align died with signal 6 (ABRT) “
What does this mean?
I am trying to match two sets of single-end reads against the reference genome (taken from ensemble)
I have first built an index:
hisat2-build someSpecies.toplevel.fa someSpeciesIndex
After extracting splice-sites:
hisat2_extract_splice_sites.py someSpecies.gtf > someSpecies.txt
I run hisat2:
hisat2 -x someSpeciesIndex --known-splicesite-infile someSpecies.txt -p 3 -1 ourRead1.fq -2 ourRead2.fq > mapped_reads.sam
Then I get the above message. The mapped_reads.sam =10,36GB
What am I doing wrong?