User: from the mountains

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Posts by from the mountains

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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 8 months ago by from the mountains60
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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 8 months ago by from the mountains60
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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 10 months ago by from the mountains60 • updated 24 days ago by ricardoguerreiro212120
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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 14 months ago by from the mountains60
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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 16 months ago by from the mountains60
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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 16 months ago by from the mountains60
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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 16 months ago by from the mountains60
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Comment: C: bedtools getfasta chromosome not found
... > ref.fa: ASCII text, with CRLF line terminators ...
written 16 months ago by from the mountains60
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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 16 months ago by from the mountains60
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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 16 months ago by from the mountains60

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