User: kk.mahsa

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kk.mahsa120
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Posts by kk.mahsa

<prev • 59 results • page 1 of 6 • next >
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Comment: C: Annotation of probes using annotated genome
... I use publicly available microarray data for meta-analysis. Plant species that I work on it have an annotated genome as the only source for probe set annotation. The annotation of probes in the Affymetrix site is very very poor and I have to use blast to the annotation of probes. How can I combine p ...
written 9 weeks ago by kk.mahsa120
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Annotation of probes using annotated genome
... Hi everyone I am trying to annotate a set of probes (Affymetrix) for a plant species. I used blastn to find the desired genome region for each probe. But the results confused me. Now I have several hits (with the same parameters such as identity and evalue) for each probe. What should I do now? Wha ...
probes annotation affymetrix microarray blastn written 9 weeks ago by kk.mahsa120
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Comment: C: Official software repository
... Thanks, it was helpful ...
written 14 months ago by kk.mahsa120
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Official software repository
... Hi I submitted a paper in a journal and they want me "Please move the long supplementary tables to an official software repository" Someone can help me introduce some official software repository to deposition of my long supplementary tables? Thanks ...
snp software repository written 14 months ago by kk.mahsa120
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A practical workflow for microarray gene expression Meta analysis
... hi and happy new year i need a practical workflow for microarray gene expression Meta analysis specially using R codes. i do not find good guideline in Google and Biostars. Anybody can help me to find a good workflow? Thanks ...
meta analysis gene expression microarray written 14 months ago by kk.mahsa120
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Comment: C: extract sequences that its identifier has specific word
... ****** nothing ***** ...
written 23 months ago by kk.mahsa120
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(Closed) extract sequences that its identifier has specific word
... hi i have a file containing various RNAs, i want to extract sequences that its identifier has mRNA word. > xxxx, mRNA AAATTT > xxxx, ncRNA TTTAA > xxxx, mRNA ATAT my output must be as below > xxxx, mRNA AAATTT > xxxx, mRNA ATA ...
fasta written 23 months ago by kk.mahsa120
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(Closed) remove space between columns
... hi i have a vcf file containing 4 columns like below. NW_012.1 35 A G now i want remove space between columns and output will be as below NW_012.135AG how can do this? ...
snp awk written 2.1 years ago by kk.mahsa120
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diffrence between number of reads in fastqc reports and collectalignmentsummarymetrics of Picard
... hi everyone i have 4 fastq files (two lane correspond to one organism), after filtration of reads, FastQC tell me that total number of reads is 628748302, i mapped them to reference genome and merged resulted two bam file and then sorted it. Now when i run collectalignmentsummarymetrics of Picard t ...
reads picard bam fastqc written 2.2 years ago by kk.mahsa120
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Comment: C: how to get common variants between two species?
... thanks but this is not what i want ...
written 3.1 years ago by kk.mahsa120

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Great Question 13 months ago, created a question with more than 5,000 views. For how can i remove duplicated variants from vcf file?
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Popular Question 13 months ago, created a question with more than 1,000 views. For error when running MarkDuplicates
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Great Question 23 months ago, created a question with more than 5,000 views. For how can i remove duplicated variants from vcf file?
Popular Question 23 months ago, created a question with more than 1,000 views. For how to combine two output of RepeatMasker?
Popular Question 23 months ago, created a question with more than 1,000 views. For bgzf_read error during samtools run
Popular Question 23 months ago, created a question with more than 1,000 views. For error when running MarkDuplicates
Popular Question 23 months ago, created a question with more than 1,000 views. For how can i remove duplicated variants from vcf file?
Popular Question 23 months ago, created a question with more than 1,000 views. For converting lowercase letters to uppercase letters in fasta file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For how can i remove duplicated variants from vcf file?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: how can i inter into my root directory in SRA (NCBI) and create subdirectory?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For how can i remove duplicated variants from vcf file?
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