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Repo info
Activity
    Nicole Suhyeon Yoon
    @lacuss
    my part is count all called transitions and then also mapping to genes (although this part we don't have post analysis)
    Allissa A. Dillman
    @allissadillman
    Right sorry I am still getting used to the github thing which file is it called? I thought it was count_mapping2gene.txt but that is just the output not the code? Sorry
    SergejN
    @SergejN
    hm, good point.. I don't see the script, either..
    Nicole Suhyeon Yoon
    @lacuss
    what do you mean?
    SergejN
    @SergejN
    is it mapping2gene.py?
    Nicole Suhyeon Yoon
    @lacuss
    mapping2gene.py
    yeah
    SergejN
    @SergejN
    okay
    Nicole Suhyeon Yoon
    @lacuss
    .txt is the result file.
    I know I shouldn't put the result in github but I thought it is good to preserve cause it is kind of final result.
    Allissa A. Dillman
    @allissadillman
    omg I am an idiot sorry
    SergejN
    @SergejN
    yeah, I agree
    Nicole Suhyeon Yoon
    @lacuss
    and hand it to Allisa
    SergejN
    @SergejN
    damn it :) Allissa, you're too fast!
    Allissa A. Dillman
    @allissadillman
    ha!
    SergejN
    @SergejN
    I agreed to Nicole :)))
    Allissa A. Dillman
    @allissadillman
    sure sure :P
    you just agreed I was an idiot
    SergejN
    @SergejN
    :P I'd never say that about the future boss
    Allissa A. Dillman
    @allissadillman
    meh I kinda think its good to tell your boss when they are being an idiot sometimes but that's just me
    SergejN
    @SergejN
    ok, I'll keep that in mind
    Allissa A. Dillman
    @allissadillman
    Hey guys I changed the Caveats of interpreting data paragraph could you read it and tell me if you follow the logic there?
    SergejN
    @SergejN
    looks ok
    Allissa A. Dillman
    @allissadillman
    cool beans
    SergejN
    @SergejN
    ok guys, I have to go now... it's 7:30pm here and I have an important soccer game to play...
    is it okay with you?
    easaki
    @easaki
    Thanks, Allissa for the carveat section.
    easaki
    @easaki
    Just got out of meeting with Ben (for another project) and he said that he was going to take the google document at the end of today, clean it up and then have everyone review it one last time. He will then send it to PLOS ONE on Wednesday.
    Allissa A. Dillman
    @allissadillman
    Sounds great, thanks everyone I think we did a great job
    Nicole Suhyeon Yoon
    @lacuss
    good to hear. Thank you! It was a great opportunity to work with you guys!
    SergejN
    @SergejN
    Hi guys! As for the aligner we used - was if hisat or bowtie after all? I'm kind of lost.. in the paper it says tophat and bowtie, but I was pretty sure we used hisat, didn't we?
    easaki
    @easaki
    I think that we were unable to get hisat to complete - like less than ten - so that's why we used the back-up of tophat and bowtie. Right, Nicole?
    I meant the "less" than ten " was for the 36 sample group.
    easaki
    @easaki
    Serjej, did you win your important soccer game?
    SergejN
    @SergejN
    yeah, we did :) thanks! However, quite some people including myself were injured :(
    but nothing bad, don't worry
    kandpal
    @kandpal
    i think, we were having technical problem with Hisat, so nicole started using tophat-bowtie for 6 sample data as backup plan. But the next day hisat’s problem got fixed so we used HISAT for same 6 samples.. we used hisat's output (6samples set) for final analysis. We also tried runing Hisat for 36 sample but were not able to complete it after 10 samples. is it right abhi/nicole?
    Allissa A. Dillman
    @allissadillman
    Hey guys sorry I am not super helpful I have been stuck home since yesterday with the flu still can't really read my screen, cold/flu season always sucks when your on immunosuppressants. In any case I haven't been able to go thru the paper one more time like I had planned but I am pretty sure we used Hisat for the 6 samples I was only doing tophat bowtie if we couldn't get hisat to work.
    SergejN
    @SergejN
    ok. get well!
    easaki
    @easaki
    OK, i missed that part about the hisat. I'll change the document unless somone else already did.
    Get better, Allissa. Also, Sergej, get better from your injuries.
    Nicole Suhyeon Yoon
    @lacuss
    @kandpal is right. but the Hisat running for 36 sampls part, we have 8 Hisat aligned results but among them, 6 samples fully finished.
    abhinav
    @nellore
    we used hisat for the six samples; the 36 samples did have something like 6 completed alignment jobs
    Genomics Infinity
    @venkataddala
    Is this group active ?
    abhinav
    @nellore
    sure
    Genomics Infinity
    @venkataddala
    Good work on mapper abhinav !!
    abhinav
    @nellore
    thanks
    Genomics Infinity
    @venkataddala
    did you tried isoforms annotations from cancer samples?
    abhinav
    @nellore
    hm, to which annotations are you referring?
    the annotations with which i'm familiar are listed here https://github.com/nellore/runs/blob/master/sra/annotation_definition.md