User: CC

gravatar for CC
CC20
Reputation:
20
Status:
New User
Location:
Melbourne, Australia
Last seen:
1 week, 1 day ago
Joined:
2 years, 10 months ago
Email:
j************@ecodev.vic.gov.au

Posts by CC

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Calculating TPM from featureCounts output
... Thank you for this explanation of how to calculate TPM. I was previously using the method described on the website linked in the question above - it gave me quite a different answer. I was wondering - is there a publication which lists the method to calculate TPM in the way you have in your answer? ...
written 26 days ago by CC20
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Comment: C: How do you identify the contigs from trinity assembly?
... Hi, I was just wondering if you ended up finding a way to annotate the contigs from Trinity? ...
written 4 weeks ago by CC20
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Krona vs MEGAN for metagenomic data
... I was wondering if someone could please explain the difference between Krona and MEGAN to me? I realise that you visualise metagenomic data with them, but do they do the same thing? I guess I'm confused because you can use a blast result file as input for both of them, but you can also use a MEGAN ...
rna-seq written 10 weeks ago by CC20
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Program that will allow me to view multiple alignments at once
... I have BAM files of reads mapped to multiple different reference sequences within the one file. Is there an alignment viewer that would allow me to view those alignments at the same time on one screen? It would be also beneficial if I could view multiple BAM files that have multiple different refere ...
alignment written 12 weeks ago by CC20
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Is there an alignment program that allows you to sort results by coverage (amount of reference sequence covered)?
... I am wanting to align reads to a database of reference sequences. This database contains thousands of reference sequences. I would like to only see the reference sequences that the reads cover a certain percentage, eg. only see the reference sequence if reads cover >50% of it. Currently, I am do ...
alignment written 11 months ago by CC20 • updated 11 months ago by Pierre Lindenbaum116k
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My run over-clustered - what does this mean for the data?
... Hi, I recently sequenced some libraries on a MiSeq, and I must have got the concentration wrong because it over-clustered. The cluster density was 1997k/mm2. The run still completed and I have data, but I was wondering what I can expect from this data/is it usable? I had a massive amount of reads ...
illumina miseq rna-seq written 15 months ago by CC20 • updated 15 months ago by genomax62k
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Comment: C: Getting BLAST to give output whilst running
... Thanks, this makes it clear. ...
written 2.9 years ago by CC20
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Comment: C: Getting BLAST to give output whilst running
... Yes, I am using a job scheduler as I am using a cluster at work. I've been told it is managed by a combination of Torque and Moab... is there a way to look at intermediate output with those schedulers? ...
written 2.9 years ago by CC20
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Getting BLAST to give output whilst running
... I run large BLAST jobs that can sometimes take days or weeks to complete. With other jobs I find I can see the output of the job as it is running, which lets me know it is working and how its progress is doing, however with BLAST it doesn't give any output until it is finished, which means I never r ...
blast written 2.9 years ago by CC20 • updated 18 months ago by biokoala3.6k

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