Platanus :PLATform for Assembling NUcleotide Sequences · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Platanus :PLATform for Assembling NUcleotide Sequences

Hi, Have someone used the software Platanus (http://platanus.bio.titech.ac.jp/) I have some problem when used the pre-processing tools platnaus_trim and platanus_internal_trim from this Platanus packages. When I run this simple command for my paired-reads: platanus_trim xxx_1.fastq xxx_2.fastq
there is not any error, but finally I get a empty xxx_1.fastq.trimmed and xxx_2.fastq.trimmed files. I really don't know what happened and need some help. Thanks!

platanus platanus_trim platanus_internal_trim

• 3,182 views • link

updated 10.1 years ago by Biostar

• written 10.3 years ago by hope •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Ribo-seq analysis workflow
written 9 months ago by mansiparihar13 •

I am working on Ribo-seq analysis workflow and the sample that I am using is a paired end sample, so when I do the pre-processing …
BAM reads much longer than fastq?
written 4.4 years ago by Jay •

I have some paired-end RNAseq data that I downloaded (so, not mine). I started with their fastq files and have run them through Trimmomatic and …
Significantly different number of reads between two paired files when runing kneaddata
written 6.2 years ago by zhangdengwei

Hi all, I am using `kneaddata` to remove the contaminated reads belonging to the host, and below is my command nohup kneaddata -i ../01.fastp/dynamics_12/clean_SAMEA2580278_r1.fq.gz -i …
Is it necessary to do FastQC before using RSEM?
written 6.9 years ago by John

Hi When I see High profile journals, some of them ran FastQC, TrimGalore , Trinity for pre-processing fastq files of RNA seq reads, some of …
SolexaQA++ lengthsort - c output
written 8.9 years ago by gtho123

I am looking for advice on the output of `SolexaQA++ lengthsort - c` when preprocessing my RNA-Seq data. Having already used `SolexaQA++ dynamictrim` to trim …
Why does STAR filter out many paired end reads while they align fine as single end?
written 9.9 years ago by KDL •

I noticed that STAR filtered out a lot of reads when they were supplied in paired end fastq files but kept both of them when …
Ray Meta assembler
written 10.2 years ago by glady

I am using Ray meta to align some paired end fastq files of my Metagenome but the output directory which is getting generated has empty …
Merging assemblies with GAM-NGS
written 10.6 years ago by pbigbig

Hi, I have 2 assemblies constructed from different libraries of same organism (PE reads 300bp and 150bp for Newbler and Platanus assembler, respectively). The Newbler …
dealing with unknown base pairs after assembly
written 12.2 years ago by Abdullah

Hi, I used MITObim to assemble a mitochondrial genome from illumina high seq paired end reads. I first merged the reads to one fastq file …
Paired-End Sequence Preprocessing Effects On Downstream Processes
written 15.2 years ago by Travis

<p>Hi all,</p> <p>I am wondering if pre-processing of paired end reads (for example to trim low quality ends & filter resulting sequences beneath a given …