User: kingcohn

gravatar for kingcohn
kingcohn20
Reputation:
20
Status:
New User
Location:
Last seen:
2 years, 2 months ago
Joined:
3 years, 10 months ago
Email:
z*************@gmail.com

Posts by kingcohn

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
921
views
1
answer
Create fasta of matched sequences with gaps
... Hello. I am attempting to isolate exons in thousands of genes using a highly fragmented draft assembly and a well curated official gene set of a closely related species. So far, I've gotten reasonable data from the program SPALN, which takes exonic regions and concatenates these in a closely related ...
gene alignment nucleotides blast fasta written 2.4 years ago by kingcohn20 • updated 2.3 years ago by lieven.sterck8.0k
0
votes
9
answers
13k
views
9
answers
Comment: C: Recommendations For Heterozygous Genome Assembly Software
... thanks, I'll ask a new question. But the directory does not. Using my own data set, the error is now failure to recognize GapCloser > spades/CPBscaffolds.fasta -o redundansCPB [ERROR] GapCloser: not found despite GapCloser in directory: ``` src/redundans >CHANGELOG.md fastq ...
written 3.7 years ago by kingcohn20 • updated 8 months ago by RamRS27k
0
votes
9
answers
13k
views
9
answers
Comment: A: Recommendations For Heterozygous Genome Assembly Software
... Hello Leszek, I am attempting to run your program but am having issues. I first installed using the pre-compiled binaries via your link and then tried to manually install all of the programs. After confirming all the dependencies have been acquired I am still getting some errors in the redudans.py ...
written 3.7 years ago by kingcohn20 • updated 8 months ago by RamRS27k
0
votes
0
answers
1.3k
views
0
answers
a5 assembly Error building contigs with IDBA
... I am using the a5 assembler to construct a de novo genome. The sample data ran without any issues but I'm getting an error with my fastq reads. [a5] Found the following libraries: raw1: id=raw1 p1=/home/molecularecology/Desktop/zcpb/raw_cp3/CPBWGS_three_1.fastq.gz ...
de novo assembly a5 a5 assembler idba error written 3.8 years ago by kingcohn20
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Issues assembling using ABySS on HTC
... Hey Benv, So, I've been able to compile and install the software on my university's HTC system. However, after running for several days there are no outputs and the system cancels my jobs. I've run other assembly softwares on the network, spades, minia...etc. without this issue. Here is the script ...
written 3.8 years ago by kingcohn20
0
votes
4
answers
2.2k
views
4
answers
Answer: A: Assembling de novo with multiple versions of paired-end reads
... Yeah, we're aware of the limitations and the data was originally designed to align with reference genome of related species via BWA , which I've done. But I am curious to see if we can assemble contigs with comparable quality without a reference, which might illustrate unique features in our system. ...
written 3.8 years ago by kingcohn20
0
votes
4
answers
2.2k
views
4
answers
Answer: A: Assembling de novo with multiple versions of paired-end reads
... Insect. It's an insect genome, well several related species each with around a genome around 1.1Giga bases*** not 30Mb, which is roughly one chromosome. Anyway, I'm attempting to first identify large genomic variations between species, then call variants among. But total coverage is pretty low at on ...
written 3.8 years ago by kingcohn20
5
votes
4
answers
2.2k
views
4
answers
Assembling de novo with multiple versions of paired-end reads
... I am attempting to assemble a 30Mega base genome using Illumina paired-end data. In order to get decent depth of coverage, the sequencing was done twice and we have four .fastq files. F & R for version one (roughly 80% coverage) and F & R for version two (~20% coverage). I'm unsure how to as ...
de novo assembly paired-end versions illumina written 3.8 years ago by kingcohn20
1
vote
1
answer
2.5k
views
1
answer
SPADES assembly failed, unequal amount of reads
... I am attempting to assemble a novel insect genome using several assemblers (abyss, spades, minia...etc). I've preprocessed the raw paired-end fastq files following the Palumbi Lab's: Simple Fool's Guide, which uses tools in the fastqtoolkit like quality trimmer, duplicate counter...etc. I also have ...
assembly paired-end spades written 3.8 years ago by kingcohn20 • updated 3.8 years ago by harold.smith.tarheel4.5k
0
votes
1
answer
1.3k
views
1
answers
Answer: A: Issues assembling using ABySS on HTC
... Hello Benv, Thanks for your reply. Yes, I installed from the source.tar and used the most recent update (2.0.0) from yesterday 9/1. This update no longer requires the sqlite library and appears to have installed properly. Tangentially, do you have any suggestions for assembling low coverage (20x) i ...
written 3.8 years ago by kingcohn20

Latest awards to kingcohn

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Assembling de novo with multiple versions of paired-end reads
Popular Question 2.3 years ago, created a question with more than 1,000 views. For SPADES assembly failed, unequal amount of reads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1873 users visited in the last hour