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User: Lina F

gravatar for Lina F
Lina F • 150
Reputation:
150
Status:
Trusted
Location:
Boston, MA
Last seen:
2 months ago
Joined:
4 years ago
Email:
l**********@gmail.com

Posts by Lina F

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Error building snpEff database "Transcript 'hypothetical_protein' already exist
... 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 4 months ago by Lina F • 150
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Comment: C: Error building snpEff database "Transcript 'hypothetical_protein' already exist
... it's GCA_001007165.2 ...
written 4 months ago by Lina F • 150
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Error building snpEff database "Transcript 'hypothetical_protein' already exists"
... 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 ...
database snpeff build written 4 months ago by Lina F • 150 • updated 4 months ago by Pierre Lindenbaum ♦ 114k
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Comment: C: Running two bedtools commands in series produces error "has non positional recor
... Thanks for the tip, this worked and let's me avoid copying things manually! ...
written 4 months ago by Lina F • 150
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Answer: A: Running two bedtools commands in series produces error "has non positional recor
... 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 4 months ago by Lina F • 150
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Comment: C: Running two bedtools commands in series produces error "has non positional recor
... Thank you for the suggestion! Unfortunately, this didn't work for me either :-( ...
written 4 months ago by Lina F • 150
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Running two bedtools commands in series produces error "has non positional records"
... 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 ...
bedtools vcf written 4 months ago by Lina F • 150
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Comment: C: Jellyfish: every other kmer count is zero
... 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 5 months ago by Lina F • 150
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Jellyfish: every other kmer count is zero
... 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 ...
jellyfish kmer counting genome size estimation written 5 months ago by Lina F • 150
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Comment: C: Visualizing whole genome alignment beyond dotplots
... 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 9 months ago by Lina F • 150

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