Questions tagged [assembly]
Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or transcripts assembly, in which case the original sequences are RNA transcripts.
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Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
user16732
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Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!
I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data.
I have the file contigs.fa from short reads but phasing step with ...
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Calculating alignment/mapping time
I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (...
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Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
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bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem.
My original command was:
...
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Determining fragment mean and fragment stdev for MaSuRCA config file
Similar to this unanswered question on Biostars, I am using MaSuRCA for the first time and want to know how other MaSuRCA users are determining fragment mean and fragment stdev. My understanding is ...
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Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
When i started programming against PDB i had a mixture of confusion & frustration with the fact that certain cif files contain two actual structures aka ...
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DNASTAR viral-host integration assembly keeps failing
I have two NGS files from an NGS company corresponding to the sequencing data from a tumor sample as follows:
TB_7710391_R1.FASTQ.gz
TB_7710391_R2.FASTQ.gz
I have downloaded the genome for MCPyV as ...
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RagTag patch error--"Tuple index out of range"
This question was also asked on GitHub
I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching long-read sections. ...
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DNA genome string reconstruction from k-mer
I have the following quiz question, but the Pattern1 for both (ACC|ATA) and (CGA|ACT) are unique (just grep for ...
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Repeat analysis on eukaryotic assemblies
I have a hundred insect genomes and I'm looking for repeated regions along these assemblies.
First of all, I thought of using <...
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Gffcompare issue: 0 reference transcripts loaded
I am trying to use gffcompare to compare my assembled transcriptome to a reference gtf that contains information about small open reading frames (sORFs). The reference gtf was obtained by processing ...
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Will using smaller kmers help get larger contigs? If not, then what?
I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas.
Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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How to manually curate a genome assembly for sequence variation or error?
I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
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