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Metavelvet not producing "meta-velvetg.contigs.fa"

assembly velvet gcc metavelvet written 13 months ago by Vimac • 0 • updated 13 months ago by WouterDeCoster ♦ 29k

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874

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Metavelvet stops at Scaffolding

software error assembly metavelvet written 2.3 years ago by biotacg • 0

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3.7k

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MetaVelvet gets stuck at "Starting pebble resolution..." step (individually and probably as a part of MetAMOS)

metamos assembly metavelvet pebble resolution written 3.6 years ago by Tim • 110 • updated 3.6 years ago by Anaïs Vittu • 0

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Appreciated to genomax ♦ 49k
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Recent Replies

C: Help interpreting Stringtie 'fully covered transcripts' output by h.mon ♦ 15k
Seems different exons of the same transcript.
C: Filtering rRNA from RNAseq data by rsafavi • 0
Thank you, I will try that
A: Please suggest an appropriate genome-guided transcriptome assembler by Kevin Blighe ♦ 21k
The one tool that is no longer recommended (even by the developers of the program) is TopHat / To...
A: Filtering rRNA from RNAseq data by igor ♦ 6.2k
There are some related suggestions in this previous thread: https://www.biostars.org/p/207311/
C: Generating network from gene expression of a cancer cell line by Kevin Blighe ♦ 21k
As many samples as you can find, I believe. Derermining 'power' in expression studies is difficul...
A: Filtering rRNA from RNAseq data by genomax ♦ 49k
You can find the mouse rDNA repeat unit [sequence here][1]. You can then use `bbsplit.sh` from BB...
A: Find the genomic position of CTCF binding site on DMPK gene by manuel.belmadani • 30
It seems like the initial report of those flanking CTCF sites are from this [paper][1]: "Recent...
C: Making Scaffolds From Contigs Without Paired Read Information by mariaveronicafumero • 0
any software to do this? (scaffolding from paired-end reads and contigs, no mate-pairs) thanks!
A: Find the genomic position of CTCF binding site on DMPK gene by Alex Reynolds ♦ 24k
Another option is to use CTCF calls for `hg38` from analysis done by [Matt Maurano's lab][1] for ...
C: Confused about merging RNA-seq lanes/runs by genomax ♦ 49k
One library is one prep done from a sample aliquot. One can make multiple libraries from a sample...
C: data pre-processing for WGCNA Algorithm by Kevin Blighe ♦ 21k
So, you have ENSEMBL gene names (begin with '*ENSG*') and you nee to convert these to HGNC / Offi...
C: Filtering rRNA from RNAseq data by Mehmet • 370
rRNA can cause to low mapping ratio of reads to genome.

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