Question: Paired-end insert size upper limit
0
gravatar for lukacdm
3.8 years ago by
lukacdm0
United States
lukacdm0 wrote:

I am mapping paired-end reads using Bowtie2 and setting "maximum insert size for valid paired-end alignments" to 500 bases. However, when I calculate the insert sizes of the resulting bam files using Picard Insert Size Metrics I frequently see one or two inserts per file that exceed 20000 bases.  Is the Bowtie2 mapping incorrectly returning very large inserts, or is the Picard software mis-analyzing the bam file?  If these large inserts are really coming from incorrect mapping, how can I remove them from the bam files so my downstream analyses are not affected?

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by lukacdm0
0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is just how the data mapped first-pass. Downstream analysis/summary tools will not consider the data as valid - so you can just leave these in the input.

Best, Jen, Galaxy team

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson25k
0
gravatar for lukacdm
3.8 years ago by
lukacdm0
United States
lukacdm0 wrote:

Thanks, Jennifer.  Will peak calling programs also ignore the long inserts?

ADD COMMENTlink written 3.8 years ago by lukacdm0

The two peak calling tools on the public Main Galaxy instance at http://usegalaxy.org only accept single-end input. So you will be running a tool on a local/cloud for this analysis.

There should be an option for this with most tools, but this is more educated guess than fact. If you are in doubt, there is usually a link to the 3rd party tool documentation on the execution/help form that will help you to determine the proper usage for the tool you are using.

Best, Jen, Galaxy team

ADD REPLYlink written 3.8 years ago by Jennifer Hillman Jackson25k
0
gravatar for lukacdm
3.8 years ago by
lukacdm0
United States
lukacdm0 wrote:

Thanks so much.  I usually use other galaxy instances that have appropriate Peak Calling programs.

ADD COMMENTlink written 3.8 years ago by lukacdm0
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