User: micro32uvas

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micro32uvas10
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Pakistan
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6 days, 2 hours ago
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3 years ago
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Posts by micro32uvas

<prev • 52 results • page 1 of 6 • next >
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Comment: C: NovoPlasty is producing identical Assemblies
... Yeah and to combat this issue, I went with Sanger for the confirmation. Turned out there was read depth problem at some locations, in case of multiple assemblies. They didn't vary much but few of them made multiple. Ruled the problem out by Sanger. ...
written 8 weeks ago by micro32uvas10
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Mitochondrial genomic analysis by PCoA, PCA and Arlequin
... Hello everyone, I have been working on the mitochondrial genome but it is not my expert field. I have extracted complete mitochondria from my whole genome sequenced samples. So far, I have used MEGA, DNASP and other related software. But I want to use Arlequin for population analysis but cannot f ...
organelle genome pca pcoa arlequin written 8 weeks ago by micro32uvas10
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NovoPlasty is producing identical Assemblies
... Hello, I have been extracting the mitochondria from my whole genome sequence data. This one sample, produced 3 assemblies, 2 of them are identical and the third one is close to the validated sequence (I did sanger to compare) It is seed and extend based and I cannot understand why it produced exa ...
assembly novoplasty mitochondria written 4 months ago by micro32uvas10 • updated 8 weeks ago by Biostar ♦♦ 20
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(Closed) Diff gene expression for knock out gene on RNA Seq data
... Hi there, I have got this RNA seq data in .csv format. doe degs. I need to find the knock out gene effect on this data. Can anyone help in a simplified manner? Awaiting your response. Ainnie NC1_length NC1_expected_count NC1_FPKM NC1_Symbol NC2_length NC2_expected_count NC2_FPKM NC2_Symbol ...
R degs knockout gene rna-seq written 8 months ago by micro32uvas10 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: BWA-mem alignment is not giving desired output
... now that i am trying with .fa indexed file. Here is the next error, that needs to be resolved: [E::bwa_set_rg] the read group line is not started with @RG and here is my read group: @A00234:29:H5LTLDMXX:2:2488:31855:37059 1:N:0:GCTGGTTA I read all the "passing a variable to the read group ...
written 12 months ago by micro32uvas10
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Comment: C: BWA-mem alignment is not giving desired output
... It just includes the intermediate processes. ...
written 12 months ago by micro32uvas10
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Comment: C: BWA-mem alignment is not giving desired output
... I am indexing the genome again with bwa. However, the command that you indicated; isnt it the same as i mentioned above? bwa mem -t 24 -M ref.fna trimmed-files1/1P.fastq trimmed-files1/2P.fastq >sample.sam 2> mem-pe.log Kindly elaborate it a little. I cannot get the desired output with t ...
written 12 months ago by micro32uvas10 • updated 12 months ago by genomax59k
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BWA-mem alignment is not giving desired output
... Hello, I have clean and trimmed fastq files with an average of 150nt per read. I have tried BWA aln and also BWA mem for the alignment with my reference genome. The alignment take around 2 days to process but ends u with 92kb file each time. I have changed algorithm from aln to mem, tried default ...
bwa-mem alignment wgs written 12 months ago by micro32uvas10 • updated 12 months ago by mittu1602150
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Comment: C: Alignment of the partial genome sequencing
... It worked perfectly. However, now that i have this partial desired mapped sequence, how can i look for the potential snps?? I can call SNPs but what about annotation. I am not clear about what possible should be done afterwards. I know its little out of this initial questions' scope, but it is jus ...
written 13 months ago by micro32uvas10
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Comment: A: Alignment of the partial genome sequencing
... I have created a bam file using bowtie2. Ref file is chr1 of the reference genome. with 2 mate pair fastq files. here is the same result: >@HD VN:1.0 SO:unsorted @SQ SN:NC_006088.4 LN:196202544 @PG ID:bowtie2 PN:bowtie2 VN:2.1.0 SRR455103.1 83 NC_006088.4 90 ...
written 13 months ago by micro32uvas10

Latest awards to micro32uvas

Popular Question 18 days ago, created a question with more than 1,000 views. For Bowtie2 alignment error
Popular Question 11 months ago, created a question with more than 1,000 views. For bowtie2-align died with signal 6 (ABRT) (core dumped)

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