Laurent -
Try the awk code again using a samtools flag "-f 0x2" instead of "-F 0x4".
There's a difference between "both ends mapped" and "mapped as a proper
pair". It might be that Picard calculates the mean insert size only for
proper pairs.
- tom blackwell -
On Fri, 5 Sep 2014, Laurent MANCHON wrote:
> --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
>
------------------------------------------------------------------------------
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
