User: williamjohn360

Reputation:
90
Status:
Trusted
Location:
Malaysia
Last seen:
4 years, 5 months ago
Joined:
6 years, 2 months ago
Email:
w*************@gmail.com

about me

Posts by williamjohn360

<prev • 21 results • page 1 of 3 • next >
0
votes
0
answers
3.6k
views
0
answers
(Closed) Free bioinformatics journals list
... What are the Journals in bioinformatics/computational biology which have free processing charge?. I am not concerned about impact factor but it should be accepted as decent publication. ...
bioinformatics journals written 4.4 years ago by williamjohn36090
0
votes
0
answers
1.2k
views
0
answers
Placing Heme in homology model protein - UCSF chimera
... I would to place heme in the homology modeled protein. (i) I tried in UCSF chimera, by loading template protein 1TQN and my homology modelled protein. (ii) Then I tried Tools option -> structural comparison -> Matchmaker (iii) Then selected Favorites option -> commoand line and I typed ...
7
votes
2
answers
4.2k
views
8 follow
2
answers
Best way to remove contaminants to get nuclear genome
... I have plant genomic reads (WGS method) through hiseq 2000 with paired-end reads (read1.fastq, read2.fastq). I need to remove chloroplast and mitchondria reads to assemble only nuclear reads. I need to know which is best and fast way to remove contaminants 1. First doing genome assembly and remove ...
genome assembly written 5.7 years ago by williamjohn36090 • updated 5.7 years ago by Adrian Pelin2.3k
0
votes
2
answers
5.4k
views
2
answers
Comment: C: Bwa or bowtie for mapping mulitple genomes
... Thanks for your answer. I can download all genome as one file through batchentrez . Can I make this one single reference genome (plastid.fa). Then I can map reads to these plastid.fa. I can get mapped reads using `samtools -F` option. Sorry, I don't understand "You can pass parameters into bowtie to ...
written 5.8 years ago by williamjohn36090 • updated 8 weeks ago by RamRS25k
0
votes
2
answers
5.4k
views
2
answers
Comment: C: Bwa or bowtie for mapping mulitple genomes
... I have paired-end genomic reads obtained from Hiseq 2000. My aim is to extract plastid reads from genomic reads by mapping to plastid genomes. Since I don't know which one is close reference to my sample. I am planning to map my reads to all plastid genome available in NCBI organelle genome resource ...
written 5.8 years ago by williamjohn36090
5
votes
2
answers
5.4k
views
2
answers
Bwa or bowtie for mapping mulitple genomes
... I have illumina paired-end whole-genome sequencing reads which I have map to around -400 reference plastid genomes. After getting mapped reads, I have to assemble as de novo plastid genome. 1. Do I have map reads to invidiual reference genomes one by one, or can I download all genomes at one go and ...
bowtie mapping bwa rna-seq written 5.8 years ago by williamjohn36090 • updated 5.8 years ago by Dan D7.0k
0
votes
2
answers
3.4k
views
2
answers
Comment: C: How To Find Novel Genes From Comparative Transcriptomics?
... Please let me know if this question is not clear. ...
written 5.9 years ago by williamjohn36090
9
votes
2
answers
3.4k
views
5 follow
2
answers
How To Find Novel Genes From Comparative Transcriptomics?
... We have sequenced from two tissue of plants which are distantly related but are from same species. I want to compare these two transcriptome of these two plants and to find novel genes by comparing two transcriptomes. How can I do that?. Any suggestions?. I am thinking on the workflow 1. Denovo as ...
transcript written 5.9 years ago by williamjohn36090 • updated 5.9 years ago by Adrian Pelin2.3k
1
vote
1
answer
3.7k
views
1
answer
Ngs-Qc-Per Base Sequence Content Failed
... I am newbie in NGS. We have sequenced non-model plant through illumina Hiseq 2000, and I have done the quality check for the raw sequence with fastqc, with fastqc quality check, the sequences passed all the test but failed in "Per Base Sequence Content". What should I do?. In what way I can improve ...
illumina qualitycontrol fastqc written 6.1 years ago by williamjohn36090 • updated 6.1 years ago by Sean Davis26k
2
votes
1
answer
2.4k
views
1
answer
Ngs-Qc & K-Mer
... I am new to NGS, I have just received sequenced raw files of non-model plant from Hiseq. I would like to know sequence quality check for quality filtering. I also like to do K-mer analysis, genome size estimation and heterozygosity rate analysis. Please let me know the best tools to do this. I have ...
qualitycontrol written 6.1 years ago by williamjohn36090 • updated 6.1 years ago by jackuser1979870

Latest awards to williamjohn360

Popular Question 5.7 years ago, created a question with more than 1,000 views. For Need Good Cytoscape Tutorial
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Ngs-Qc-Per Base Sequence Content Failed
Popular Question 5.7 years ago, created a question with more than 1,000 views. For How To Find Novel Genes From Comparative Transcriptomics?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Constructing Pathway With List Of Gene Using Cytoscape
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Bwa or bowtie for mapping mulitple genomes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 795 users visited in the last hour