--Hi,
For tophat, i need to fix parameter "-r" i.e. inner distance (instead of
the insert size) which is insert-length - 2*readLength.
So, i have mapped my paired-end reads(read length=100) to the reference
genome with bowtie2, then i used Picard's CollectInsertSizeMetrics.jar
tool to estimate the insert size
to then set the mate inner distance parameter in tophat (-r), this is
the output of picards tools:
MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE
MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS
PAIR_ORIENTATION W
IDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT
WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT
WIDTH_OF_70_PERCENT WIDTH_OF_
80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE
LIBRARY READ_GROUP
163 38 82 269356442 180.122413 69.468016
66668352 FR 15 31 45 61 77 95
113 135 247 3777
now if i use another method to compute 'mean insert size' and 'standard
deviation' directly from the bam file:
samtools view -F 0x4 File.mapped.bam | awk '{if ($9 >0)
{sum+=$9;sumsq+=$9*$9;N+=1}} END {print "mean = " sum/N " SD="
sqrt(sumsq/N - (sum/N)**2)}'
i obtain: mean = 6486.58 SD=806658
In the second method mean insert size is vastly different from that
obtained in the first method with picard tool.
Do you think I might be doing something wrong here ? Is there another
tool to compute the correct mate inner distance ?
thank you --
------------------------------------------------------------------------------
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
