User: Lina F
Lina F • 150
- Reputation:
- 150
- Status:
- Trusted
- Location:
- Boston, MA
- Last seen:
- 4 months, 1 week ago
- Joined:
- 4 years, 3 months ago
- Email:
- l**********@gmail.com
Posts by Lina F
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... Thank you, this worked! However, now it's finding other non-unique names... looks like I will have to run this fix a few times. Thanks! ...
written 6 months ago by
Lina F • 150
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... it's GCA_001007165.2 ...
written 6 months ago by
Lina F • 150
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... Hi all,
I am trying to build a snpEff database but I'm running into the following error message:
java.lang.RuntimeException: Transcript 'hypothetical_protein' already exists
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.add(SnpEffPredictorFactory.java:135)
at ...
written 6 months ago by
Lina F • 150
• updated
6 months ago by
Pierre Lindenbaum ♦ 116k
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... Thanks for the tip, this worked and let's me avoid copying things manually! ...
written 6 months ago by
Lina F • 150
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... I found a potential workaround. First, I upgraded `bedtools` from `v2.26.0` to `v2.27.1`. This changed the error message that was reported and made it easier to interpret:
Error: unable to open file or unable to determine types for file A_and_B.vcf
- Please ensure that your file is TAB ...
written 6 months ago by
Lina F • 150
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... Thank you for the suggestion! Unfortunately, this didn't work for me either :-( ...
written 6 months ago by
Lina F • 150
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... Hello all,
I have three samples, generated Illumina PE reads for each of them, and then mapped the reads against the reference to produce three alignments. I called SNPs and now I would like to determine the subset of SNPs that are present in sample A and B but not in C. I ran `bedtools` as follows ...
written 6 months ago by
Lina F • 150
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... I double checked and I did not double up my input fastq files. However, I am using both fwd and rev read files.
In total I have 29.5 million read pairs. Should I downsample this?
EDITED to add: I just ran the code with only the FWD read files and now I get 1mers and odd kmers in general.
I realize ...
written 7 months ago by
Lina F • 150
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... Hi all,
I found a tutorial suggesting how to use Jellyfish to estimate genome size:
http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html
However, after running `jellyfish count` and `jellyfish histo` the output shows that every other kmer count is zero.
Below is my code, trying several v ...
written 7 months ago by
Lina F • 150
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... Yes, I have two de novo assemblies from long read data.
I actually also have Illumina data (I used it to error-correct the assemblies) but my main question here is what kind of differences exist between the two assemblies. ...
written 11 months ago by
Lina F • 150
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