User: mail2steff

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mail2steff50
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Potsdam, Germay
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Posts by mail2steff

<prev • 47 results • page 1 of 5 • next >
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Converting tab or txt file into gxl file using R programming
... Dear All, I have a tab delimited file with following columns > otu1 otu2 counts > OTU_1 OTU_2 0 > OTU_1 OTU_3 1 > OTU_1 OTU_4 1 : : : here otu1 is the source node and otu2 is the target node. count is the ...
gxl text r programming written 17 days ago by mail2steff50
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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 19 months ago by mail2steff50
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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 19 months ago by mail2steff50 • updated 19 months ago by Sej Modha4.5k
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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 20 months ago by mail2steff50
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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 21 months ago by mail2steff50
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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 21 months ago by mail2steff50
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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 21 months ago by mail2steff50
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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 21 months ago by mail2steff50
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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 21 months ago by mail2steff50
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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 21 months ago by mail2steff50

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Popular Question 17 months ago, created a question with more than 1,000 views. For How to identify and count multi-exon genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Annotations for use with MISO and sashimi_plot

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