can you get what does my adviser mean please?

Question

[zizigolu]

Hi dudes,

My adviser asked me:

Is it possible to read from the outputs of tophat2 that how many are the multimapped reads case by case?

I watched all of tophat log files but I could not find anything, just

Reads:
          Input     :  13213023
           Mapped   :  12859856 (97.3% of input)
            of these:   1107059 ( 8.6%) have multiple alignments (75843 have >20)
97.3% overall read mapping rate.

Do you have any suggestion or idea please?

Thank you

[Ashutosh Pandey]

What you mean case by case? In above example, the following line "1107059 ( 8.6%) have multiple alignments (75843 have >20)" represents stats about the reads that have multiple mapping positions.

[zizigolu]

Thanks Ashutosh, I should asked him about case by case meaning

[h.mon]

I think your supervisor wants you to examine all multi-mapped reads, that is, he wants to know, for each one of the 1,107,059 reads with multiple alignments, where did they map.

Or do you have several BAMs, and "case by case" means multi-mapped reads for each different BAM?

[zizigolu]

thank you

actually i could not get him then i emailed him and asked him..

[zizigolu]

yeah you were all right...he wants to examine several BAMs