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1.1k

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Metavelvet stops at Scaffolding

software error assembly metavelvet written 3.3 years ago by biotacg • 0 • updated 8 months ago by RamRS ♦ 21k

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730

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

assembly velvet gcc metavelvet written 2.0 years ago by Vimac • 0 • updated 2.0 years ago by WouterDeCoster ♦ 39k

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3.9k

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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 4.5 years ago by Tim • 110 • updated 4.5 years ago by Anaïs Vittu • 0

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Appreciated to Devon Ryan ♦ 90k
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Recent Replies

A: RVTests cmc beta coefficient by pampana.akhil • 0
hey @caragh, i know its a very old message, but have you got solution for this? Please do let me ...
C: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo by O.rka • 90
Do you recommend a method for checking the quality of an assembly vs. transcriptome besides mappi...
A: Protein coding annotation from UCSC by Luis Nassar • 100
Hello Tim, With your same selections on the [Table Browser][1], if you change the **output forma...
C: What skills are required for an informatics scientist? by genomax ♦ 67k
`Informatics scientist` is a rather broad term that could potentially include the kitchen sink of...
C: Trouble installing Bioconda by genomax ♦ 67k
Bioconda appears to be installed correctly. `ddocent` [is only available on linux and macOS][1]. ...
C: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo by O.rka • 90
What other stats would be useful to add here? I think the only one `STAR` outputs regarding this ...
A: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo by swbarnes2 ♦ 5.5k
"Too short" usually means "didn't map". Are you sure this is an appropriate reference genome? H...
C: Tools To Calculate Average Coverage For A Bam File? by macielrodriguez2 • 10
I ran: samtools depth zm_cp.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}' and the...
C: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo by Damian Kao ♦ 15k
Try setting --outFilterMatchNmin to 20 to see if you can get more mapping. However, that means it...
C: Tools To Calculate Average Coverage For A Bam File? by macielrodriguez2 • 10
Does this also works with mpileup? I ran: samtools mpileup zm_cp.bam | awk '{print $4}' | pe...
C: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo by lieven.sterck ♦ 4.7k
can you provide some stats on the input fastq file you are using?
C: what does the bed file in bedtools multicov command refer to ? by geek_y ♦ 9.6k
The chip-seq data is usually represented as peaks of genomic coordinates in bed file format.

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