User: from the mountains

Reputation:
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New User
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United States
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2 days, 23 hours ago
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3 years, 10 months ago
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Posts by from the mountains

<prev • 44 results • page 1 of 5 • next >
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Comment: C: How to change filtering parameters in gff3 -> gtf conversion using gffread?
... i'm not sure if this answers my question. The input examples i show are both transcript features and their gbkey is transcript as well. How come one is retained in output.gtf but the other isn't? ...
written 5 weeks ago by from the mountains40
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How to change filtering parameters in gff3 -> gtf conversion using gffread?
... I'm trying to convert a gff3 to gtf with gffread and i'm seeing unexpected filtering of most records in the gff3. it is for a viral genome. Only 10 out of 180 are going through. curiously, the first of these two records are converting, but the second is not: EF999921.1 Genbank transcript 60089 ...
software error data formatting written 5 weeks ago by from the mountains40
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pacbio-illumina hybrid assemblies
... We are looking into assembly with pacbio and illumina data, and wondering if there are any tools or well-validated workflows for hybrid assemblies, as well as any recommendations for coverage. this is for a eukaryotic genome. additionally, has anyone ever tried a pacbio-10XGenomics hybrid assembly? ...
assembly illumina pacbio hybrid assembly written 3 months ago by from the mountains40
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any tool to join reads regardless of overlap?
... I'm hoping to find a tool that will merge reads if there's a non-ambiguous overlap, and join the rest of the reads with some symbol, like a number of hyphens or NNNNs. I vaguely remember finding a tool that can do it but now I can't remember. Help is appreciated! ...
merging written 7 months ago by from the mountains40
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Comment: C: bedtools getfasta chromosome not found
... for some reason my answer posted above, i'm not sure how to move it: `00000000 54 47 47 54 47 47 41 54 47 43 54 47 0a 3e 43 50 |TGGTGGATGCTG.>CP|` `00000010 30 31 34 35 39 34 0a 41 43 41 47 43 43 47 41 43 |014594.ACAGCCGAC|` `00000020 41 41 43 43 43 41 41 43 41 54 47 43 43 41 41 41 |AAC ...
written 9 months ago by from the mountains40
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Comment: A: bedtools getfasta chromosome not found
... `00000000 54 47 47 54 47 47 41 54 47 43 54 47 0a 3e 43 50 |TGGTGGATGCTG.>CP| ` `00000010 30 31 34 35 39 34 0a 41 43 41 47 43 43 47 41 43 |014594.ACAGCCGAC|` `00000020 41 41 43 43 43 41 41 43 41 54 47 43 43 41 41 41 |AACCCAACATGCCAAA|` `00000030 43 54 43 43 41 47 41 43 54 43 47 41 41 43 ...
written 9 months ago by from the mountains40
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Comment: C: bedtools getfasta chromosome not found
... good catch! unfortunately, it still doesn't work, in spite of both files now being ASCII text with no \r . ...
written 9 months ago by from the mountains40
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Comment: C: bedtools getfasta chromosome not found
... > ref.fa: ASCII text, with CRLF line terminators ...
written 9 months ago by from the mountains40
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bedtools getfasta chromosome not found
... I am getting a curious error when using bedtools to extract sequences from a reference fasta and a gff3 file. I enter: `/gpfs/gwngs/tools/bedtools2/bin/bedtools getfasta -s -fullHeader -fi ref.fa -bed ref.gff3` And I get a million lines saying, for example: > WARNING. chromosome (CP014594) w ...
software error bedtools sequencing written 9 months ago by from the mountains40
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Comment: C: genemark-es gene-finding with reference and annotation
... thanks for your reply. I think I was misinterpreting the quast manual--i think that *after* I liftover an annotation so it corresponds to the new assembly, i could feed both the new assembly and the new annotation into quast and to report those genes plus new genes that aren't in the new annotation ...
written 9 months ago by from the mountains40

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