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elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
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Multi sample calling error #9

Closed clemgoub closed 7 years ago

clemgoub commented 7 years ago

Hello,

I am encountering an issue while trying to do a multi-sample calling. I did successfully called the polymorphic TE in 15 samples independently, then as indicated in the tutorial, filtered the gff3 using the filtering tool with the automatically generated parameter files. I am now using the multisample_caller.sh script as detailed in the manual, but I have the following error:

Error: Sorted input specified, but the file MScalling.all_filtered.gff3 has the following out of order record chr10 jitterbug TE_insertion 53046175 53046292 . . . supporting_fwd_reads=21; supporting_rev_reads=16; cluster_pair_ID=167; lib=None; Inserted_TE_tags_fwd=AluYe5, AluYc, AluY, AluYe6, AluYk3, AluYf1, AluSc, AluSx1; Inserted_TE_tags_rev=AluYe5, AluYk3, AluYk2, AluY, AluSx; fwd_cluster_span=234; rev_cluster_span=327; softclipped_pos=(53046206, 53046215); softclipped_support=3; het_core_reads=0; zygosity=1.000; predicted_superfam=AluYe5 *

The process seemed to have stopped and only the file .all_filtered.gff3 is not empty. I have to add that the filtering has been very drastic, since only one or two line has been kept per file out of ~2000 or more initial calls!

Thanks for your reply!

Clément

mbosio85 commented 7 years ago

Hi

there was a bug in multisample tool because mergeBed require the input file to be sorted. Now I added an extra line, can you try to update the code with git pull and rerun it?

About the filtering strictness you can manually edit the filtering parameters (also removing them) if you want from the filter text file.

Mattia

clemgoub commented 7 years ago

Hi Mattia!

Excellent it worked lika a charm!

Thanks a lot!