Hi
I have some data from RNAseq which I'm going to map using tophat, but because I don't know the inner mate distance I'm mapping using bowtie2 to get to know this inner distance between reads (I took a subset of 25000 reads from the original data).
The problem I'm having is related to the output, I find it little bit weird and I can't find the column with the inner mate distance (which should be the number 9). And by the way, I'm new into this data.
This is the bowtie2 line:
Log
First two lanes of sam file
Thanks.
I have some data from RNAseq which I'm going to map using tophat, but because I don't know the inner mate distance I'm mapping using bowtie2 to get to know this inner distance between reads (I took a subset of 25000 reads from the original data).
The problem I'm having is related to the output, I find it little bit weird and I can't find the column with the inner mate distance (which should be the number 9). And by the way, I'm new into this data.
This is the bowtie2 line:
Code:
bowtie2 --sensitive -x /local/Reference/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -1 Panc042_PDAC_PRITUM_Px00__raw_RNAseq_R1_SUBSET25000.fastq -2 Panc042_PDAC_PRITUM_Px00__raw_RNAseq_R2_SUBSET25000.fastq -S bowtie2_subset/Pan042_PDCA_PRITUM_Px00_raw_RNAseq_subset.sam &> bowtie2_subset/log_bowtie2.txt
Code:
25000 reads; of these: 25000 (100.00%) were paired; of these: 7297 (29.19%) aligned concordantly 0 times 12786 (51.14%) aligned concordantly exactly 1 time 4917 (19.67%) aligned concordantly >1 times ---- 7297 pairs aligned concordantly 0 times; of these: 2039 (27.94%) aligned discordantly 1 time ---- 5258 pairs aligned 0 times concordantly or discordantly; of these: 10516 mates make up the pairs; of these: 5801 (55.16%) aligned 0 times 3773 (35.88%) aligned exactly 1 time 942 (8.96%) aligned >1 times 88.40% overall alignment rate
Code:
HWI-ST1391:130419:D22RGACXX:4:1101:1389:2058 83 chr7 115578630 42 75M = 115578540 -165 GATACAAGCTAAGCCTGAGATAATTATTATACAATAAGGATTTACTATTTTTCTCCTTTTATCAGCATTAGGGTC EFC=F@@8)88(?*BIIIIIGDG@GCFD?:0:***?C??:9??1?>GEEBAA3<+AEEDE<C<$ HWI-ST1391:130419:D22RGACXX:4:1101:1389:2058 163 chr7 115578540 42 75M = 115578630 165 TCGGGCTTTAATGACTGTACCCAGAAGTTAGTAATTATTTTTCCATGTCAAACAATAAAATTATTTTAATTCTCC 1=:=+=@AFAA4CBE,<+<AEGC88AAFEC41:?C<9:C:DGEII4?*009BG;D/9B>>==B$
Thanks.
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