User: kozhaki.seq

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kozhaki.seq50
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Posts by kozhaki.seq

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Method to identify tissue specific genes in plant species?
... I never come across the article. Thanks @microguge ...
written 13 months ago by kozhaki.seq50
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Method to identify tissue specific genes in plant species?
... I have microarray dataset consists of different tissue expression profiles from **oryza sativa (rice)**. I was using clustering analysis (for ex, k-means clustering) to find tissue specific genes. Is there any better/alternative method or package available for finding tissue specific genes? FYI ...
bioinformatics microarray statistics written 13 months ago by kozhaki.seq50
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Comment: C: Error: gtf_to_fasta returned an erro - Is there any better Rice gtf file for RN
... Thanks @genomax2. I will make a try..!! ...
written 23 months ago by kozhaki.seq50
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Comment: C: Error: gtf_to_fasta returned an erro - Is there any better Rice gtf file for RN
... Thanks for reply @genomax2. I checked the link which you provided. But the files looks the older one. As I know MSU has version 7 now and IRGSP build 5 is available . Do you have any comments? ...
written 23 months ago by kozhaki.seq50
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Error: gtf_to_fasta returned an erro - Is there any better Rice gtf file for RNAseq is available?
... Recently I updated tophat pipeline to tophat2 and and bowtie2. I was trying to working on DEGs in Oryza sativa (japonica species) using Illumina paired end reads and got the error "Error: gtf_to_fasta returned an error".   tophat2 --GTF all.gff3.txt -o result2 riceindex 5D-con1_1_val_1.fq 5D-con1_ ...
rice software error forum next-gen rna-seq written 23 months ago by kozhaki.seq50 • updated 21 months ago by Biostar ♦♦ 20
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Answer: A: Mapping of gene
... You can use GenomePixelizer (http://www.atgc.org/GenomePixelizer/GenomePixelizer_Welcome.html)  to map your genomes to chromosome. Unlike Circos (http://circos.ca/), the tool generate linear chromosome image and the best thing is 'tool generates HTML codes which can be used for making clickable imag ...
written 2.0 years ago by kozhaki.seq50
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Comment: C: Gene list for an organism
... Since you have not mentioned the organism, Ensembl might have the list of genes of your genome of interest. You can use Biomart for the extraction of feature. Pls check : http://asia.ensembl.org/biomart/martview/ad8ed8fe2fb53d008ee8ecbdbbdf1340 For the plant genome: http://plants.ensembl.org/bioma ...
written 2.1 years ago by kozhaki.seq50
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Comment: C: BLAST multiple sequences against each other from one FASTA file
... Here is how my note on BLAST run, Make a directory, enter the directory. Keep database file and input file inside it. 1. Make index files for the database : makeblastdb -in indica.fasta  -dbtype prot  -out indica 2. Blast your sequence against the database: blastp -query japonia.txt -db indica -o ...
written 2.1 years ago by kozhaki.seq50
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Comment: C: Finding most co-expressed genes of input gene based on Pearson correlation
... Yes, since my matrix dimension is high, I am concern about the time..Yes, I will look into it @Sam ...
written 2.1 years ago by kozhaki.seq50
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Finding most co-expressed genes of input gene based on Pearson correlation
... I have a matrix of microarray (around 30000 genes X 800 samples) as a back-end data set. In the workflow, if someone input a gene of their interest, I need to find it's highly co-expressed genes based on back-end data set. For that, I need to calculate pairwise Pearson correlation of input gene agai ...
pearson correlation pairwise microarray written 2.1 years ago by kozhaki.seq50 • updated 2.1 years ago by Zhilong Jia1.1k

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