Paired reads and mitochondria sequence

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Paired reads and mitochondria sequence

Post by ptranvan on Thu May 19, 2016 4:53 pm

Hi, I have few questions about dnaPipeTE usage.

1) If we have PE reads, what is the best strategy ? Use only R1 reads or pool together R1 + R2 ?

2) About mitochondria sequence:

IMPORTANT: We recommend to remove from your reads mitochondrial and other none nucleic DNA, such as known symbionts or guts' bacterias. We found that if mitochondrial reads are left in the samples, RepeatMasker will annotate the corresponding conting to "Gypsy-12_DVir-I LTR/Gypsy" with however a weak score.

It will just affect the final pie chart right ?

3) My goal is to fetch TE sequences (output in Trinity.fasta), where can I find the correspondance among header and TE class ? for example >comp0_g1_i1 = LINE etc.


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Re: Paired reads and mitochondria sequence

Post by Clément Goubert on Mon Jun 27, 2016 6:39 pm

Hi,

1) I would recomend to use only one end (R1 or R2 files) since sampling among a mix of R1 and R2 may be uneven because of the paired nature of the data.

2) Actually the mtDNA can be recognized by dnaPipeTE as TE (with however weak score) so it can artificially inflates the proportion of some TE class and thus lead to biased estimates if you don't use an annotation threshold.

3) You'll be able to find the correspondence in the sorted RepeatMasker table: ./Annotation/oneRM_hit_per_Trinity_contig (not sure about the exact spelling of this file Shocked )
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