Top Tweets for #TAMAtools
@melanie_sagniez @martinalexsmith @gringene_bio @mikelove @FairlieReese Thank you for the response! What is the RNA library in this plot? Have you tried contacting the TALON folks for parameter suggestions? Also have you tried #TAMAtools?(https://t.co/trJC0Xqg4E) Note that TAMA should never be run default.
This is cool! But just note that you can use TAMA Merge with a reference. You just treat it as another source to merge and give it top priority. #tamatools
It's #bioinformatics Friday and here's my work in progress - how to handle multiple @PacBio Iso-Seq samples. Feedback welcome! https://t.co/fNWg66RrRN
A new and improved oyster genome using @pacbio, Iso-Seq and Hi-C. A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas https://t.co/74tcOGAw3B
I will also extensively cover the use of #TAMAtools. TAMA, admittedly, has a steep learning curve but once you understand how it works, it is extremely versatile! This is a great chance to get a real understanding of how to fully take advantage of TAMA!
4/n
Trick or treat? The #TAMAtools paper is finally out! Thank you to all the authors @Yuanyuan929 @runxuan John W.S. Brown @smithjac7 @AlanArchibald51 @DavidBurt8
https://t.co/uwLBgCAJve
Heads up! I'll be taking part in the @UCD_Bioinfo Iso-Seq workshop with @Magdoll and @anaconesa next week! I'll be running a section on #TAMAtools . I think there is still time to register: https://t.co/BvYjR5yQF5
#GI2020 #TAMAtools For anyone interested I have a poster for today's session "P56 - Identifying novel genes in the human genome using TAMA long read RNA sequencing analysis". It's a bit short but I'll be available for any TAMA questions during the poster session.
Another fantastic study using #TAMAtools ! From @SimoneMeddle @hindlemm @DavidBurt8 @Yuanyuan929 @KasiaM44369499 and collaborators:
https://t.co/V9ut3CJCt8
#TAMAtools I added a tool a few weeks ago but forgot to add the manual to the wiki (just added). The tool is "tama_remove_fragment_models.py" and it removes possible truncated transcript models from your annotation. https://t.co/8gsowfLYvA
Just updated #TAMAtools repo. Added a low memory run mode for TAMA Collapse which drastically reduces memory usage and speeds it up a bit. Compromise is no variant calling with low mem mode. Also fixed CIGAR format issue for "Minimap2 -a" runs. https://t.co/trJC0Xqg4E
Another awesome study using #TAMAtools! Honored for TAMA to be of use to @bat1kgenomes @Sonja_Vernes @EmmaTeeling1 @BatLabUCD @hillermich @TheGeneMyers @ZixiaH
https://t.co/pH20BnGANk
I asked my dad to update the #TAMAtools code to python 3.
2 questions:
1. Is this ethical?
2. How do I acknowledge him with respect to institution affiliation in future talks? (He is retired)
Looks good. Parallels with (some of the functionality of) our colleague @GenomeRIK's #TAMAtools for PacBio data? Thoughts Richard?
I'll be giving a quick presentation on #TAMAtools at the Virtual Nanopore Day, Edinburgh. If you use @nanopore cDNA or direct RNA sequencing, you might be interested. I will also share some of my benchmarking results. https://t.co/QdCZLt6VhE
Some great work on the dog genome! Thank you @OWallerman for using #TAMAtools! https://t.co/Iq0eI7nU4P
I just pushed an update for the #TAMAtools github repo. I saw that a few people recloned after this. There are some new tools which I will post wiki pages for this weekend. Also new columns for the TAMA Merge transcript and gene report files.
@aarzalluz_ @PacBio Thanks for the bump! Looking forward to integrating #TAMAtools with SQANTI/TAPPAS/IsoAnnot (and future tools)!
#SMRTLeiden Erich Jarvis brings up issues with differentiating between paralogs and haplotypes/alleles when analyzing RNAseq data. How do we know where the transcript models actually represent on the genome? #TAMAtools has a way of looking at this. See https://t.co/s1GUVBTjpy
Some other group just made a bioinformatic tool called TAMA:
https://t.co/eiGKxEjsDm
What's the etiquette for dealing with tool name copying?
Thanks to @ralfcmueller for the heads up!
#TAMAtools
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