User: karthick.n

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karthick.n10
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Posts by karthick.n

<prev • 9 results • page 1 of 1 • next >
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GTF to GFF conversion
... Can someone suggest me some command line for the conversion of GTF to GFF in linux ? I could see only the conversion of GFF to GTF in the forum. Thanks in Advance! Karthick ...
htseq rna-seq written 5 days ago by karthick.n10 • updated 5 days ago by Juke-343.1k
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Pair Orientation in IGV
... I'm new to genomics platform. When I was analyzing the alignment data in IGV i came across the word "Pair Orientation"with values "F1R2", "F2R1". I don't know what they are. Can someone explain what these values are? Thanks in advance! - Karthick ...
genome assembly next-gen gene sequencing written 11 days ago by karthick.n10
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Comment: C: Undefined variable error in linux
... Thanks a lot Amar :) For your responses! ...
written 23 days ago by karthick.n10
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Comment: C: Undefined variable error in linux
... Hi Sir, This is the command for variant calling: gatk HaplotypeCaller -R hg19.fa -I NA12878.sort.mkdup.bam -O NA12878.gatk.raw.vcf --max-alternate-alleles 1 ...
written 24 days ago by karthick.n10
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Comment: C: Undefined variable error in linux
... Thanks a lot Mr.Pierre. Yes. Few of the variants don't have that attribute. Is it because of the improper variant calling? Should I need to do variant calling again? Also, how to remove those variants from the vcf file. Kindly provide your answer. Thanks in advance! :) Have a great day ...
written 24 days ago by karthick.n10
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Comment: C: Undefined variable error in linux
... Hi Amar, Thanks a lot for your quick response! I'm using the latest version of gatk (v4.1.4.0) only. Also modified the command based on your input, but still the system throwing the same error. :( . This is the modified command. gatk VariantFiltration -R hg19.fa -V NA12878.gatk.raw.vcf -O NA1287 ...
written 24 days ago by karthick.n10
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Undefined variable error in linux
... Hi, I am running the following command in Linux for variant filteration: *gatk VariantFiltration -R hg19.fa -V NA12878.gatk.raw.vcf -O NA12878.gatk.raw.flag.vcf -filter “DP < 10.0” --filter-name “LowDP” -filter “QD < 2.0” --filter-name “QD” -filter “MQ < 40.0” --filter-name “MQD” -filter ...
sequencing seq linux gatk written 24 days ago by karthick.n10 • updated 24 days ago by Pierre Lindenbaum124k
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Comment: C: What is the difference between left alignment and right alignment?
... Thanks a lot for your quick response ! ...
written 24 days ago by karthick.n10
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What is the difference between left alignment and right alignment?
... I'm totally new to genomics. I have come across the words Left Alignment and Right Alignment. I know what is alignment but I don't know the difference between left & right alignment. Kindly resolve my doubt. Thanks in advance! ...
genome assembly sequence sequencing written 26 days ago by karthick.n10 • updated 26 days ago by Jean-Karim Heriche21k

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