hi,everyone
I updated tophat from 1.1.4 to 1.2.0,newest version recently.
Then I run tophat1.2.0 giving the same paired-end reads, but the mapping rate decreased to 22% from 37%(using tophat1.1.4) .
Is this because that 1.2.0 has become able to support Indels?
But this Indel-detection is disable as default
(it is needed to give '--allow-indels' option to enable this function,but i didin't..)
Actually tophat1.2.0 output insertions.bed and deletions.bed which are both empty. With --allow-indels option, however,these files were not empty(59K,89K).
Would somebody please explain this result for me?
Thanks in advance.
#I'm not good at English.
#so if my English make you feel bad, I'm so sorry.
I updated tophat from 1.1.4 to 1.2.0,newest version recently.
Then I run tophat1.2.0 giving the same paired-end reads, but the mapping rate decreased to 22% from 37%(using tophat1.1.4) .
Is this because that 1.2.0 has become able to support Indels?
But this Indel-detection is disable as default
(it is needed to give '--allow-indels' option to enable this function,but i didin't..)
Actually tophat1.2.0 output insertions.bed and deletions.bed which are both empty. With --allow-indels option, however,these files were not empty(59K,89K).
Would somebody please explain this result for me?
Thanks in advance.
#I'm not good at English.
#so if my English make you feel bad, I'm so sorry.
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