User: Lina F
Lina F • 100
- Reputation:
- 100
- Status:
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- Location:
- Boston, MA
- Last seen:
- 1 day, 8 hours ago
- Joined:
- 2 years, 10 months ago
- Email:
- l**********@gmail.com
Posts by Lina F
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C: Duplicates on Illumina
... Has this been resolved, and if yes, how? I checked some of our recent NextSeq runs and it seems to not be a problem. Thanks!! ...
written 1 day ago by
Lina F • 100
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C: SPAdes is running out of memory
... FYI: I was able to run bbnorm using the example you linked to and reduce the input illumina dataset to about 25 million read pairs. SPAdes was then able to assemble the data (using eight threads).
Thanks again for the feedback and suggestions, it was very helpful! ...
written 5 days ago by
Lina F • 100
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C: SPAdes is running out of memory
... I checked my illumina data and this does not seem to be a problem with this sample. However, I will spot check samples from some other runs and from our other NextSeq machine as well. ...
written 5 days ago by
Lina F • 100
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C: SPAdes is running out of memory
... Had not seen this -- thanks for sharing! ...
written 6 days ago by
Lina F • 100
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Comment:
C: SPAdes is running out of memory
... 2x150bp from a NextSeq... I just started running bbnorm ;-) ...
written 6 days ago by
Lina F • 100
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C: SPAdes is running out of memory
... yes, that number is very large! I am not entirely sure what the units are but the math doesn't seem to work out either way :-/ ...
written 6 days ago by
Lina F • 100
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Comment:
C: SPAdes is running out of memory
... Thanks for the suggestions!
My Illumina data is 139,240,211 read pairs, and I have 100,661 reads from the minIon. I am not sure about predicted coverage -- do you have a suggestion on how to calculate that?
I will try capping SPAdes at 8 threads and will also take a look at downsampling my input d ...
written 6 days ago by
Lina F • 100
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... Hi all,
I tried running a hybrid assembly for a fungal genome. I have one set of PE reads from Illumina and a MinIon dataset. It should be about 45 Mbases when complete. I ran it on a machine with 35 cores and 250 Gb of RAM.
I am running SPAdes v 3.10.1 and it errorred out with error code "-6" and ...
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Answer:
A: Issues installing bcl2fastq?
... I took some notes last time I installed bcl2fastq and this worked for me on Ubuntu. However, it's an older version, so feel free to modify:
SOURCE_NAME=bcl2fastq2-v2.17.1.14.tar.zip
SOURCE_URL=ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/$SOURCE_NAME
SOURCE ...
written 8 days ago by
Lina F • 100
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... Hi all,
I'm interested in attending a workshop to learn more about how to process minion data and hybrid assemblies (illumina + pacbio or minion long reads).
If you can recommend a workshop or an upcoming conference, I'd love to hear about it!
Thanks! ...
written 8 days ago by
Lina F • 100
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