Chimeric.out.junction file issues in segment 2 co-ordinates

[User_new]

I have single end reads and did 

STAR --runThreadN 8 --genomeDir $TRANS_DATA --readFilesIn $TRANS_DATA/5_S5_R1_001_trimmed.fq --outSAMtype BAM Unsorted --outFileNamePrefix chim --alignIntronMin 1 --chimSegmentMin 20 and get 

When I look at the first segment say for example from line I get 841 - 891 , however for the second segment I always get 1971 - 1972 (meaning just a difference of 1). What am I doing wrong? I would like to get the start and end of both segments of the chimeras.

[Alexander Dobin]

Hi @User_new

col 5 (e.g. 1971) is the last base of the intron of the chimeric junction, so the second segment starts at the next base (i.e. 1972).

Cheers

Alex