User: mail2steff

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mail2steff30
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New User
Location:
Potsdam, Germay
Last seen:
1 week, 1 day ago
Joined:
2 years, 6 months ago
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m*********@gmail.com

Posts by mail2steff

<prev • 44 results • page 1 of 5 • next >
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Comment: A: Creating Interactive Volcano Plots with R and Plot.ly
... Dear Dr.Kelly, I have executed the above script with the Gfold values (similar to logfold2 change). since we are working with non replicated data, we don't have a p value. Thus, I would like to have +fold change on x axis and -fold change on y axis. I am able to get the graph but a regular scatter ...
written 10 days ago by mail2steff30
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Comment: C: Generation of Consenses Fasta from SAM/BAM
... Ive found many posts dealing with samtools mpileup -uf reference.fa aligment.bam | bcftools view -cg - | vcfutils vcf2fq But I am not looking for any SNP or INDELS. Can I proceed with the same command? ...
written 29 days ago by mail2steff30
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Comment: C: Generation of Consenses Fasta from SAM/BAM
... I got only 60% of alignment percentage through bwa mem. My sample and reference are not so different. they belong to same species. Thats y I wanna find out microstatellites. ...
written 29 days ago by mail2steff30
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Generation of Consenses Fasta from SAM/BAM
... Dear All, I have a SAM file which I got it from bwa mem (whole genome Data). My next step is to annotate the repeats using Repeat masker and to identify microstatellites using misa. For both MISA and Repeat Masker, I need fasta format. I tried to convert bam file to fasta format. But the result is ...
fasta ngs bam misa sam written 29 days ago by mail2steff30
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Comment: C: Bowtie Alignment with scaffold assembled reference genome
... Hi Vijay, I tried with bwa mem. In that I got 55% alignment. How can I interpret this? ...
written 4 weeks ago by mail2steff30
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Comment: C: Bowtie Alignment with scaffold assembled reference genome
... Ive updated my post. Kindly check it. I have 17766 fasta headers in my file and total number of bases in my reference genome is 370418818 ...
written 4 weeks ago by mail2steff30
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Bowtie Alignment with scaffold assembled reference genome
... Dear all, I got the whole genome sequences of a papaya variety. And I downloaded the ref genome (Carica papaya) from NCBI (scaffold level assembly). When I check for the quality of my sequences, everything is fine except for the Sequence Length Distribution. When I run bowtie without trimming I g ...
ngs alignment papaya bowtie written 4 weeks ago by mail2steff30
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Comment: C: How to identify gene list present in Whole genome sequencing data?
... ##species Carica papaya contig_23646 phytozomev11 gene 5096 5506 . - . ID=evm.TU.contig_23646;Name=evm.TU.contig_23646 contig_23646 phytozomev11 mRNA 5096 5506 . - . ID=PAC:16429340;Name=evm.TU.contig_23646.3;pacid=16429340;longest=1;Parent=evm.TU.contig_23646 contig_23646 phytozomev ...
written 6 weeks ago by mail2steff30
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Comment: C: How to identify gene list present in Whole genome sequencing data?
... I downloaded papaya reference genome in fasta file from NCBI and did alignment using Bowtie2 ...
written 6 weeks ago by mail2steff30
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How to identify gene list present in Whole genome sequencing data?
... Dear All, I am new to Whole genome sequencing analysis. I have two sample fastq files. I have run fastqc and bowtie2 using reference genome (papaya). I got the sam file. Now How to computationally identify the list of genes and their locations present in my file. I need all the gene list. So I can ...
gene prediction samtools whole genome sequencing written 6 weeks ago by mail2steff30 • updated 6 weeks ago by JC6.5k

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