User: el97004

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el9700410
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Posts by el97004

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kmer counting for heterozygosity estimation
... Hi all, I want to count kmers in my sequencing reads inorder to be able to estimate heterozygosity of my genome using [Genomescope][1]. I have paired end reads (R1.fastq, R2.fastq), I ran [Jellyfish][2] to count kmers using the following settings: jellyfish count -C -m 21 -s 5000000 -t 8 R1.fastq ...
heterozygosity kmer jellyfish genome assembly written 6 months ago by el9700410 • updated 6 months ago by Dattatray Mongad350
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Comment: C: Command to parse mummer coords file
... Thanks! cut -c fixes the issue, I will paste the final working code below: cat coords | tail -n +3 | cut -c 63-71 | awk '{ total += $1 } END { print total/NR }' ...
written 9 months ago by el9700410
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Comment: C: Command to parse mummer coords file
... Assuming my file is named "coords" cat coords \ | tail -n +3 \ # remove header section | cut -f 10 \ # get %IDY column (I think this is where it fails) | awk '{ total += $2; count++ } END { print total/count }' # average calc ...
written 9 months ago by el9700410
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Command to parse mummer coords file
... Hi ! Anyone know some linux commands that can be used to parse through the output coords table of [MUMmer][1]? It has the following output format: [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS] ============================================================ ...
mummer nucmer written 9 months ago by el9700410 • updated 9 months ago by Pierre Lindenbaum129k
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Comment: C: Redundans: no pairs aligned
... I will try those two things. Thank you for the help! ...
written 9 months ago by el9700410
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Comment: C: Redundans: no pairs aligned
... Just ran repair.sh from BBMap successfully on my reads. Unfortunately the message persists even after doing this. ################################################## [Wed Oct 30 16:48:25 2019] Scaffolding... iteration 1.1: run1/contigs.reduced.fa 603 4122740 34.603 204 3945123 44917 586 ...
written 9 months ago by el9700410
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Comment: C: Redundans: no pairs aligned
... But I just double checked and both read files (R1 and R2) have the same number of reads in them. Is there any other way to test that they are in "sync" ...
written 9 months ago by el9700410
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Comment: C: Redundans: no pairs aligned
... Thanks for the suggestion! They were trimmed together but i do have a step where I remove reads that map to certain scaffolds (scaffolds that are not part of my target organism (contamination)) and so I think this might be what is causing it ...
written 9 months ago by el9700410
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Redundans: no pairs aligned
... Hello, Does anyone know what would cause "No paris were aligned!" message during the scaffolding step in Redundans? I am running it using this command: redundans.py --identity 0.70 -v -i R1.fastq R2.fastq -f contigs.fa -o Results I've checked all of the documentation and the examples to see ...
redundans assembly written 9 months ago by el9700410
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Comment: C: Interpret genome alignment results
... Thank you that makes sense. But how about in less extreme case scenarios, for example if the third codon in the DNA is mutated it could have no affect on the protein sequence ...
written 9 months ago by el9700410

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