tophat2 some parameters are not working (--no-novel-indels and -a)

[statsteam]

I used tophat2 to map reads with --no-novel-indels and -a 6 parameters. Once the mapping is done, I examined the result (accepted_hits.bam) and found some lines with indels or some lines whose anchor length < 6.

## with insertion
SRR074943.46688543 369 chr1 10178 0 21M2I27M chr14 69256332 0 CCTAACCCTAACCCTAACCCTAAAACCCTAACCCTAACCCTAACCCTAAC <<;@=ABA=A=BAB7B8B>B?ABA=BBB4B8BBB<B8BBC?B=BBCABBB AS:i:-11 XN:i:0 XM:i:0 XO:i
:1 XG:i:2 NM:i:2 MD:Z:48 YT:Z:UU NH:i:16 CC:Z:= CP:i:10184 HI:i:0


## anchor length < 6
SRR074943.63823907 329 chr1 14825 0 5M140N45M * 0 0 GATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGATATCAAGT BBBBBBBBBB?A@@B@>BB?:><<?@@?=?<:9@<6:=65:?:7:=:=4, AS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42C7 YT:Z:UU XS:A:- NH:i:7 CC:Z:c
hr15 CP:i:102516151 HI:i:0


There are a lot of lines like these. I am wondering if anyone else had the same problem as this or I did something wrong in running tophat.

This is the command line I used to run tophat2

tophat -o tophat_out -N 3 -r 30 --mate-std-dev 110 -a 6 -I 300000 -p 8 -g 20 --no-novel-indels --no-coverage-search hg19_index read_1.fastq read_2.fastq

Thank you!

[statsteam]

I figured out -a 6 parameter issue. It does not ensure individual read to have at least x bps on each side of junction. Instead, it ensures that each junction to have at least one read that meet the anchor condition. If -a 6 is used, each junction must have reads that spans at least 6bps on each side of junction.

I still do not know why --no-novel-indels does not work.