User: Satyajeet Khare
Satyajeet Khare • 1.3k
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Posts by Satyajeet Khare
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Comment:
C: RNA-seq Data Excel Formatting
... You can use any simple text editor to get your genes of interest in this format
`goi_1|goi_2|goi_3` etc. Next, try `grep` like this
grep -E "goi_1|goi_2|goi_3" expression_matrix.txt
You can also save the output as
grep -E "goi_1|goi_2|goi_3" expression_matrix.txt > output.txt ...
written 6 weeks ago by
Satyajeet Khare • 1.3k
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... The issue is resolved. I made two changes. I don't know which one worked.
1. I had skipped the local realignment step earlier. That is, I had used the `Picard` output directly for BQSR. I corrected the pipeline by incorporating that step.
2. I used genome.fasta and all .vcf files from gatk resourc ...
written 9 weeks ago by
Satyajeet Khare • 1.3k
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... Thanks, I will try running without `-an QD` parameter, but here are a couple of other peculiar observations.
1. I do see QD annotations in my VCF file, even without running the `VariantAnnotator` also.
2. If I try and validate the resource VCF files from [gatk resource bundle][1] (1000G and hapmap) ...
written 9 weeks ago by
Satyajeet Khare • 1.3k
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... Mine is a small dataset (4 samples). Is that the problem? Should I just shift to hard filtration such as this?
QD<2.0||MQ<40.0||FS>60.0||MQRankSum<-12.5||ReadPosRankSum<-8.0 ...
written 9 weeks ago by
Satyajeet Khare • 1.3k
• updated
4 weeks ago by
RamRS ♦ 20k
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... Thanks @toralmanvar. I tested the input vcf file like this
java -jar GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Homo_sapiens.GRCh38.dna.primary_assembly.fa --variant:VCF gatk_out/output_annotated.vcf
The command finished the run without any errors. But the ou ...
written 9 weeks ago by
Satyajeet Khare • 1.3k
• updated
4 weeks ago by
RamRS ♦ 20k
3
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... I am performing trio analysis with Exome sequencing data.
I am using GATK 3.8.
I am at VariantRecalibrator stage. Following is my command...
java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -input /gatk_out/output.vcf --resource:hapmap,known= ...
written 9 weeks ago by
Satyajeet Khare • 1.3k
• updated
4 weeks ago by
Biostar ♦♦ 20
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... This worked fine for me.
java -jar GenomeAnalysisTK.jar -T ValidateVariants --reference_window_stop >= 300 -R Genome.fa --variant:VCF All.vcf.gz ...
written 11 weeks ago by
Satyajeet Khare • 1.3k
0
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... Assuming that the data you need is not available on any other platform, you may want to use colorspace reads directly for the analysis. No need to convert the reads. You can use Tophat with bowtie1 option. Use bowtie version 0.12.7 or lower. ...
written 4 months ago by
Satyajeet Khare • 1.3k
1
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337
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... For Affy ST arrays, you can use `oligo` `read.celfiles` function like this...
> rawData <- read.celfiles(celFiles)
You can try normalization
> Data <- rma(rawData)
And finally try annotation on normalized data
> Data <- annotateEset(Data, hugene10sttranscriptcluster.db)
You m ...
written 11 months ago by
Satyajeet Khare • 1.3k
0
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1.5k
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Comment:
C: CRAM vs BAM
... Partly covered [here][1]. Actually CRAM is recommended for long term storage. See [here][2].
[1]: https://www.biostars.org/p/106047/
[2]: https://www.uppmax.uu.se/support/user-guides/using-cram-to-compress-bam-files/ ...
written 11 months ago by
Satyajeet Khare • 1.3k
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