User: from the mountains
from the mountains • 40
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Posts by from the mountains
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... 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 6 weeks ago by
from the mountains • 40
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... `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 6 weeks ago by
from the mountains • 40
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... good catch! unfortunately, it still doesn't work, in spite of both files now being ASCII text with no \r . ...
written 6 weeks ago by
from the mountains • 40
0
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... > ref.fa: ASCII text, with CRLF line terminators ...
written 6 weeks ago by
from the mountains • 40
1
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... 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 ...
written 6 weeks ago by
from the mountains • 40
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... 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 7 weeks ago by
from the mountains • 40
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... 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 ...
written 8 weeks ago by
from the mountains • 40
• updated
8 weeks ago by
lieven.sterck • 1.2k
1
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... 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.
...
written 4 months ago by
from the mountains • 40
• updated
4 months ago by
finswimmer • 1.5k
0
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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 5 months ago by
from the mountains • 40
0
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... I hope all is well. I have a quick question about my STAR -> stringtie -> cuffcompare workflow. I found it odd that there were no frags of type "j" when I typed the following:
$ cut -f4 ${sample}.tracking | sort | uniq -c
3864 =
14532 c
27422 e
25872 i
801 ...
written 5 months ago by
from the mountains • 40
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