User: mail2steff

gravatar for mail2steff
mail2steff50
Reputation:
50
Status:
New User
Location:
Potsdam, Germay
Last seen:
4 months, 4 weeks ago
Joined:
3 years, 1 month ago
Email:
m*********@gmail.com

Posts by mail2steff

<prev • 46 results • page 1 of 5 • next >
0
votes
1
answer
297
views
1
answers
Comment: C: Increase the kmer size in IDBA_UD?
... Dear Sej Modha, Thank you for the commands. I increased the kmer value as above mentioned and the set the increment of k-mer of each iteration as 20. Eventhough I got the contigs for the kmwe 20, 40, 60, 80 and 100. Not more than that. Will IDBA_UD produce contigs upto 100 or AM I missing something ...
written 7 months ago by mail2steff50
0
votes
1
answer
297
views
1
answer
Increase the kmer size in IDBA_UD?
... Dear all Ive pair-end reads from papaya samples with average length of 151 bp. I used IDBA_UD for assembling. I increased the read length and kmer size by changing the default value as follows static const uint32_t kMaxShortSequence = 200; static const uint32_t kNumUint64 = 16; ./idb ...
illumina ngs idba_ud idba kmer written 7 months ago by mail2steff50 • updated 7 months ago by Sej Modha3.9k
0
votes
0
answers
18k
views
0
answers
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 8 months ago by mail2steff50
0
votes
0
answers
372
views
0
answers
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 8 months ago by mail2steff50
0
votes
0
answers
372
views
0
answers
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 8 months ago by mail2steff50
2
votes
0
answers
372
views
0
answers
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 8 months ago by mail2steff50
0
votes
0
answers
397
views
0
answers
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 8 months ago by mail2steff50
0
votes
0
answers
397
views
0
answers
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 8 months ago by mail2steff50
0
votes
0
answers
397
views
0
answers
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 8 months ago by mail2steff50
0
votes
1
answer
341
views
1
answers
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 9 months ago by mail2steff50

Latest awards to mail2steff

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1278 users visited in the last hour