Hello All,
My lab has gotten two runs of mouse genome sequences from two genomes. Both runs are paired end sequenced, once with 36bp and once with 100bp. Unfortunately the people from the sequencing core who actually ran the sequences are unresponsive and the people from my lab who coordinated with them are long gone.
Now I am trying to pick up the sequencing project. So far there are SNPs and InDels from samtools, and SVs from GASV and BreakDancer. BreakDancer and samtools were run by others so I am not sure what parameters they received. I have several issues that I am looking for help on:
(1) I checked the deletions called by Breakdancer and GASV using the samtools sequence viewer, and found that reads often map in the called deletions, but have a lower quality. Does anyone have any sanity check suggestions for working with SVs from GASV and BreakDancer?
(2) I suspect that some of the deletions are due to transposable element insertions in the reference and vice versa. I would like to find the transposable element insertions, but don't know of any tools out there for doing this. Do you guys know of any? If not, does anyone have a suggestion for how to pull out of BAM files only the paired reads with one end mapped?
--> This last part is what I am struggling with because I don't even know how the BAM files were made and what was included. Also I heard that sometimes unmapped reads get the same coordinate as the mate, would this hurt my situation or is there a flag that I could use?
These are just two of my most pressing troubles, but please let me know if you have any suggestions. Thank you in advance for any help.
My lab has gotten two runs of mouse genome sequences from two genomes. Both runs are paired end sequenced, once with 36bp and once with 100bp. Unfortunately the people from the sequencing core who actually ran the sequences are unresponsive and the people from my lab who coordinated with them are long gone.
Now I am trying to pick up the sequencing project. So far there are SNPs and InDels from samtools, and SVs from GASV and BreakDancer. BreakDancer and samtools were run by others so I am not sure what parameters they received. I have several issues that I am looking for help on:
(1) I checked the deletions called by Breakdancer and GASV using the samtools sequence viewer, and found that reads often map in the called deletions, but have a lower quality. Does anyone have any sanity check suggestions for working with SVs from GASV and BreakDancer?
(2) I suspect that some of the deletions are due to transposable element insertions in the reference and vice versa. I would like to find the transposable element insertions, but don't know of any tools out there for doing this. Do you guys know of any? If not, does anyone have a suggestion for how to pull out of BAM files only the paired reads with one end mapped?
--> This last part is what I am struggling with because I don't even know how the BAM files were made and what was included. Also I heard that sometimes unmapped reads get the same coordinate as the mate, would this hurt my situation or is there a flag that I could use?
These are just two of my most pressing troubles, but please let me know if you have any suggestions. Thank you in advance for any help.
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