User: Satyajeet Khare

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Satyajeet Khare1.3k
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Posts by Satyajeet Khare

<prev • 278 results • page 1 of 28 • next >
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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 Khare1.3k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... 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 Khare1.3k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... 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 Khare1.3k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... 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 Khare1.3k • updated 4 weeks ago by RamRS20k
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... 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 Khare1.3k • updated 4 weeks ago by RamRS20k
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ERROR MESSAGE: QD annotation at VariantRecalibrator
... 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= ...
gatk variantrecalibrator snp written 9 weeks ago by Satyajeet Khare1.3k • updated 4 weeks ago by Biostar ♦♦ 20
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Comment: C: Reference allele is too long message GATK
... 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 Khare1.3k
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Comment: C: Convert colorspace fastq to basespace fastq
... 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 Khare1.3k
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Answer: A: match gives me all NA in annotating my genes
... 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 Khare1.3k
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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 Khare1.3k

Latest awards to Satyajeet Khare

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Popular Question 4 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Too low mapping percentage using HISAT2 on human reference genome.
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Popular Question 11 months ago, created a question with more than 1,000 views. For Replace XLOC id with gene symbol in FPKMmatrix function
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Differentiall analysis of chip-deq data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
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Scholar 14 months ago, created an answer that has been accepted. For A: error in tophat2
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