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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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filtering #109

Closed jasmineja closed 3 weeks ago

jasmineja commented 4 weeks ago

Hi, since I am looking for non canonical insertions I would like to keep events with no polyA, those are filtered out during the xtea run. How can we change the filtering parameters ?

simoncchu commented 3 weeks ago

Hi, there are different levels of intermediate outputs that don't require there must be a polyA, although it's a strong feature. For example, candidate_disc_filtered_cns.txt and candidate_disc_filtered_cns.txt.high_confident. But note that, xtea is designed to detect those active retrotransposon generate polymorphic insertions, not for any insertions contain a transposon portion.

jasmineja commented 3 weeks ago

Thank you very much for taking time to answer promptly. It is really appreciated. I hope it help me to detect more events. Where can I find the details of the columns of these intermediate files ? the column name ? Jasmine

On Sat, Jun 8, 2024 at 7:48 PM Simon C Chu @.***> wrote:

Hi, there are different levels of intermediate outputs that don't require there must be a polyA, although it's a strong feature. For example, candidate_disc_filtered_cns.txt and candidate_disc_filtered_cns.txt.high_confident. But note that, xtea is designed to detect those active retrotransposon generate polymorphic insertions, not for any insertions contain a transposon portion.

— Reply to this email directly, view it on GitHub https://github.com/parklab/xTea/issues/109#issuecomment-2156100885, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADE2R5LNGJDDXBCR3VSMR73ZGMYWJAVCNFSM6AAAAABIX7RKNWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJWGEYDAOBYGU . You are receiving this because you authored the thread.Message ID: @.***>

--

Jasmine Jacob-Hirsch

972-3-5304547

972-52-3790500

Functional Genomics- Head

Cancer Research Center

Sheba medical center

jasmineja commented 3 weeks ago

Moreover, if you are looking for somatic insertions , as you will when using the option of case-ctrl mode, you might miss many of those that occur in alternative processes ( not all the insertions are TPRT), if you filter out all those without poly A. Jasmine

On Sat, Jun 8, 2024 at 7:48 PM Simon C Chu @.***> wrote:

Hi, there are different levels of intermediate outputs that don't require there must be a polyA, although it's a strong feature. For example, candidate_disc_filtered_cns.txt and candidate_disc_filtered_cns.txt.high_confident. But note that, xtea is designed to detect those active retrotransposon generate polymorphic insertions, not for any insertions contain a transposon portion.

— Reply to this email directly, view it on GitHub https://github.com/parklab/xTea/issues/109#issuecomment-2156100885, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADE2R5LNGJDDXBCR3VSMR73ZGMYWJAVCNFSM6AAAAABIX7RKNWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJWGEYDAOBYGU . You are receiving this because you authored the thread.Message ID: @.***>

--

Jasmine Jacob-Hirsch

972-3-5304547

972-52-3790500

Functional Genomics- Head

Cancer Research Center

Sheba medical center

simoncchu commented 3 weeks ago

You can use the first two columns as the insertion location. It doesn't require must have the TPRT features, but xtea is not designed to detect general insertions.