User: dmathog

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dmathog30
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Posts by dmathog

<prev • 18 results • page 1 of 2 • next >
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SSPACE-longreads run behavior?
... I tried to use SSPACE-longread to scaffold the output of Platanus using 13X PacBIO coverage. The genome of the organism is around 1Gbp. The input scaffolds from platanus contain 521597 entries, 945Mbp, and has an N50 of 22573. Ran the program like this: nice perl ~/src/SSPACE-LongRead_v1-1/S ...
assembly written 4 months ago by dmathog30
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Heterozygous genome assembly software: actions on regions with copy number more than 2X?
... The general question is this: what do platanus and redundans (or any other similar programs) do when they encounter a sequence segment with copy number greater than 2X? The methods suggested in the preceding discussion https://www.biostars.org/p/63047/ all address the reduction of both copies of ...
genome assembly polymorphic written 5 months ago by dmathog30
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trnascan seqfaults and other issues
... Downloaded unpacked and built tRNAscan-SE-1.3.1 Had some problems trying to run the underlying program trnascan-1.4. First issue, it segfaults on a header like ">scf7180000558994" because its fasta reading code is looking only for a space to terminate the name, and there isn't one. Changed tha ...
software error sequence written 9 months ago by dmathog30
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Comment: C: SRA File Content
... Given a list of SRR's and a little bit scripting one can build an automatic downloader based on this sort of command: curl https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1772703 2>/dev/null | grep hdf5 ...
written 12 months ago by dmathog30
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Comment: C: Minimus2 dropping reads which perfectly match two adjacent input contigs
... I don't think this is related, but between writing the *contig and *singletons files AMOS overwrote the original *.fasta file. The new one has only 297665 entries, named >1 to >297665. So it is probably a good idea to keep a differently named copy of the input file if it is at all difficult ...
written 13 months ago by dmathog30
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Minimus2 dropping reads which perfectly match two adjacent input contigs
... Minimus2 is for some reason dropping from the final assembly long reads which match some input contigs perfectly. These reads end up in the singletons file. The input s1_s2.fasta file had 472178 haplotype specific contigs followed by 2215057 Megareads from MaSuRCA2. These are corrected PacBIO ...
assembly written 13 months ago by dmathog30
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Comment: C: Three different VCF callers ignoring the same columns with variants
... With one small tweak, that worked very well. Changed clearfilters to clearfilters minreads=5 to keep the spurious miscalls out of the variant file. Where are the various filters documented? Is there a percentage based equivalent of minreads? The desired acceptance condition for varian ...
written 13 months ago by dmathog30
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Comment: C: Three different VCF callers ignoring the same columns with variants
... > For testing, I ran BBMap's variant caller, and it also ignores that > variant. Why? It only appears once in a read with mapq>3 Out of curiosity, does BBMap act like the other three programs, calling column 178 if that one base is changed in the reference? The mapped reads were corrected ...
written 13 months ago by dmathog30
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Comment: C: Three different VCF callers ignoring the same columns with variants
... Tried this samtools mpileup -Buf scf_7180000354095.fasta scf7180000354095.bam \ | bcftools call -vmO z -o scf7180000354095.bcftoolsB2.vcf.gz and it still skipped column 178. **-E** didn't help either. Changing **m** to **c** in bcftools also didn't do it. This is samtools 1-4, by th ...
written 13 months ago by dmathog30
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Comment: C: Three different VCF callers ignoring the same columns with variants
... Yes, that is the right region. (There are many others.) ...
written 13 months ago by dmathog30

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