User: from the mountains

Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 month ago
Joined:
3 years, 8 months ago
Email:
a************@gmail.com

Posts by from the mountains

<prev • 42 results • page 1 of 5 • next >
0
votes
0
answers
117
views
0
answers
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? ...
1
vote
0
answers
204
views
0
answers
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 5 months ago by from the mountains40
0
votes
1
answer
553
views
1
answers
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 7 months ago by from the mountains40
0
votes
1
answer
553
views
1
answers
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 7 months ago by from the mountains40
0
votes
1
answer
553
views
1
answers
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 7 months ago by from the mountains40
0
votes
1
answer
553
views
1
answers
Comment: C: bedtools getfasta chromosome not found
... > ref.fa: ASCII text, with CRLF line terminators ...
written 7 months ago by from the mountains40
1
vote
1
answer
553
views
1
answer
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 7 months ago by from the mountains40
0
votes
1
answer
392
views
1
answers
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 7 months ago by from the mountains40
1
vote
1
answer
392
views
1
answer
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 7 months ago by from the mountains40 • updated 7 months ago by lieven.sterck2.6k
1
vote
1
answer
425
views
1
answer
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 10 months ago by from the mountains40 • updated 10 months ago by finswimmer6.2k

Latest awards to from the mountains

Popular Question 4 months ago, created a question with more than 1,000 views. For How is Tophat installed?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to run an identity-by-descent calculation on plink with a p-value threshold?
Popular Question 13 months ago, created a question with more than 1,000 views. For How is Tophat installed?
Popular Question 14 months ago, created a question with more than 1,000 views. For How is Tophat installed?
Great Question 19 months ago, created a question with more than 5,000 views. For How do I run Tophat?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How is Tophat installed?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How do I run Tophat?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1222 users visited in the last hour