User: from the mountains

Reputation:
40
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New User
Location:
United States
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1 month, 4 weeks ago
Joined:
3 years, 5 months ago
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Posts by from the mountains

<prev • 41 results • page 1 of 5 • next >
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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 12 weeks 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 4 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 4 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 4 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 4 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 4 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 4 months ago by from the mountains40
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genemark-es gene-finding with reference and annotation
... I have generated a new fungal assembly on a species that has been assembled before, and I am trying to translate the annotations from the old assembly to the new assembly using genemark-es within quast. The quast manual says "If a gene file is provided with -G as well, both # genes in the file cover ...
assembly gene prediction dna-seq written 4 months ago by from the mountains40 • updated 4 months ago by lieven.sterck1.9k
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BBMerge saving unmerged reads
... Is there any way to save the unmerged reads to separate files when using bbmerge? I am attempting to merge reads with overlap using bbmerge, but would also like to save unmerged reads, preferably separately to R1 and R2 files. ...
bbmerge sequencing written 7 months ago by from the mountains40 • updated 7 months ago by finswimmer3.6k
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Comment: C: Is biomaRt service down?
... I get an error like this: Error in .postForm(curl, .opts, .params, style) : embedded nul in string: '\r\n\r\n\r\n\t\r\n\tKaspersky Endpoint Security 10 for Windows\r\n\t\r\nhtml,body{height:100%}\r\n\r\nbody{width:100%;min-height:100%;margin:0;padding:0;color:#2C2C2C;font:normal 11px taho ...
written 8 months ago by from the mountains40

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