Hi Guys,
I don't get it..here's the prep read info from tophat 2.04
left_min_read_len=100
left_max_read_len=100
left_reads_in =15696378
left_reads_out=15695101
right_min_read_len=100
right_max_read_len=100
right_reads_in =15696378
right_reads_out=14783689
Here's the flagstat...
rna-ctrl-001-5-accepted_hits.statBam
30790076 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
30790076 + 0 mapped (100.00%:nan%)
30790076 + 0 paired in sequencing
17077256 + 0 read1
13712820 + 0 read2
23679570 + 0 properly paired (76.91%:nan%)
26248024 + 0 with itself and mate mapped
4542052 + 0 singletons (14.75%:nan%)
466020 + 0 with mate mapped to a different chr
65746 + 0 with mate mapped to a different chr (mapQ>=5)
tophat -G ./Genes/genes.gtf -r 100 --mate-std-dev 50 -p 16 -o ./5refAnnot --b2-sensitive --no-novel-juncs ./5_Index-8.001_VEH_CNTL_R1.fastq ./5_Index-8.001_VEH_CNTL_R2.fastq
Why is there 2X the number of single reads (left + right...). I would expect more like around 15M mapped reads!?
Thanks for your comments/explanations.
R
I don't get it..here's the prep read info from tophat 2.04
left_min_read_len=100
left_max_read_len=100
left_reads_in =15696378
left_reads_out=15695101
right_min_read_len=100
right_max_read_len=100
right_reads_in =15696378
right_reads_out=14783689
Here's the flagstat...
rna-ctrl-001-5-accepted_hits.statBam
30790076 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
30790076 + 0 mapped (100.00%:nan%)
30790076 + 0 paired in sequencing
17077256 + 0 read1
13712820 + 0 read2
23679570 + 0 properly paired (76.91%:nan%)
26248024 + 0 with itself and mate mapped
4542052 + 0 singletons (14.75%:nan%)
466020 + 0 with mate mapped to a different chr
65746 + 0 with mate mapped to a different chr (mapQ>=5)
tophat -G ./Genes/genes.gtf -r 100 --mate-std-dev 50 -p 16 -o ./5refAnnot --b2-sensitive --no-novel-juncs ./5_Index-8.001_VEH_CNTL_R1.fastq ./5_Index-8.001_VEH_CNTL_R2.fastq
Why is there 2X the number of single reads (left + right...). I would expect more like around 15M mapped reads!?
Thanks for your comments/explanations.
R
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