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Part of the problem is this:
https://github.com/merenlab/anvio/blob/50edb9265ced734070e0f57c130f6c90ea5adfd1/bin/anvi-get-sequences-for-hmm-hits#L73
But I bet that this is just the tip of the iceb…
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Does this version still support outputting bigwigs and BED files? Epic did this with -b but in SICER2 -b is bin size instead. Thanks!
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Hi Felix, it's me again.
I have RRBS data set from a NextSeq run, one from breast cancer (human) and one from vid plants.
I already had mentioned this experiments in a previous thread:
https://git…
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Hi Shujun,
I assembly a 335M diploid plant genome by Falcon-Unzip with 100x PacBio Sequel data, contig N50 9M. After using HiC data, I get chromosome-scale length genome with scaffold N50 32M.
…
baozg updated
5 years ago
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Hi Felix,
I have a questions concerning my data; I'm sorry if it's a stupid question, I'm new to WGBS data, and trying bismark to do the analysis.
I have WGBS data, PE, sequenced using the stand…
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Sergey,
I ran into a problem with the consensus step with a recent assembly (canu1.8 - installed as a conda module: https://anaconda.org/bioconda/canu). A quick query on github identified that othe…
pjm43 updated
5 years ago
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When attempting to browse https://hub.sd2e.org/user/sd2e/design/Strain_5_MG1655_Genomic_pBADmin/1 , it stalls for a long time before failing with a web page reading:
````
Error
TypeError: Cannot …
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Hi- I'am running clonalframeML on a Linux mint distribution 18.2 Sonya
It download and compiled just fine - my alignment has many ambiguous sites, as I was unsure if the algorithm could handle ambi…
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Hello Felix,
I have some single-end RRBS reads, using Illumina TruSeq primers, from human tissue I know to be positive for HBV. I am attempting to use Bismark to align viral reads from among the h…
Apb58 updated
6 years ago
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Hi,
I'm on the contig/scaffolding stage of my assembly for which we can set the `n` parameter, affecting the number or pairs there are needy to link two sequences
I was wondering how one should ac…