Closed roomfortwo closed 3 years ago
Hi, I don't have experience with RNA-seq data, is the complete mitogenome covered by it, or just certain areas? Does it only extend with poly A/T at the ends when no further extension is possible , or you think further extension is possible? You can run with extended log to 1 and send me that file, can have a look
Hi,
Here you have three logs from assemblies of the same library (SRR3458647), different seeds, the RNA from this library was selected for poly-A tails.
log_extended_hans-3-k29.txt log_extended_node49-k29.txt log_extended_scu-b-k29.txt
This in the other hand is a log from a whole RNA sequencing library (I have a bigger logs but they are too heavy), with this library I assembled the whole mtDNA. log_extended_mtDNA-frl2015-39.txt
Let me know what you think, cheers,
How long are those mitochondrial genomes you try to assemble?
And the example of your first comment is not one of those 3 you send I guess?
I don't think it is always polyA tail problem, the coverage seems to go to almost 0 before the polyA starts, so not sure if it can extend further And I think some are just A-repeats, looks like the data has a strong error rate and reduced coverage around these regions.
If you have a specific sequence or polA you want me to check i will do, but I can't check all files completly
Hey, I'm trying to assemble 14k genomes and the "strong error rate" you mention I believe are the NUMTs. If you think Novoplasty it's not extending due to low coverage and the strong variation, I'll take it.
Thank you so much for you insight!
Hi, NUMTs are not the problem, I usually doesn't affect the assembly. I mean strong error rate around single nucleotide repeats, depends on the library preparation and illumina kit you used.
Hello there, I'm using novoplasty to recover some arthropod mitochondrial genomes from RNA-seq (quite trending these days) and I'm encountering that novoplasty tends to extend the poly-A tails from the reads (or poly-T in the 3'). Example below.
>Contig01+195792442 TTTTTTTTTTTTTTTTTTTTTTTTTTATCTAGATACAACTTCCAATATATCTACTTTGTTACGACTTATCTCTTTTTTCAGAGAGAGCGACGGGCGATATGTACATAATCTAGCCCTAATTCATTAGAATAAATTAATATCTAATTACAT ... CAACATAATTTTCCTCCAGCCGATCATACGTACAATCAATTAAGTGTTTCATCTTTATAAAAAAAAAAAAAAAAAAAAA
I tried to remove the polyA/polyT sections from the reads and failed mainly because trimmers tend to remove AT-rich biological sequences of interest. I was wondering if there's any flag I could implement in which I could either soft clip the polyA extensions or just ignore them in order to retrieve genomic seqs.
Thanks in advance, Luis AF.