User: Seigfried

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Seigfried70
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Posts by Seigfried

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Comment: C: Renaming Bcftools lsec for multiple runs
... Thank you @genomax for the edits. I need to specify there is an option `-o $i.vcf`. This gives me one of the output files and if i specify -p i get 3 outputs. Thank you. ...
written 11 days ago by Seigfried70
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Renaming Bcftools lsec for multiple runs
... Hello! I have a reference file x.vcf.gz I also have multiple query files say 1y.vcf.gz 2y.vcf.gz 3y.vcf.gz .... 603y.vcf.gz I want to intersect the reference with each separate query file. Since I have the query files all in one folder, I did for i in *. ...
bcftools isec written 11 days ago by Seigfried70 • updated 11 days ago by genomax87k
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GATK finding rare variants
... Hello all I have 600 samples from which I have obtained SNPs following the GATK HaplotypeCaller step. My goal is to find rare variants across these 600 samples and visualize them. For example, a heatmap where the X axis has the samples and the Y axis has the different variant sites . This means ...
gatk written 11 weeks ago by Seigfried70
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Comment: C: GATK BaseRecalibrator Step
... Thank you for your help! I will try to find if I can find a way to replace in BAM files. Thanks a lot! ...
written 11 weeks ago by Seigfried70
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Comment: C: GATK BaseRecalibrator Step
... samtools idxstats SRR7621519_splitncigar.bam NC_000001.11 248956422 164233 0 NT_187361.1 175055 9 0 NT_187362.1 32032 0 0 NT_187363.1 127682 0 0 ... NT_187686.1 215732 0 0 NT_187687.1 170537 0 0 NT_ ...
written 11 weeks ago by Seigfried70
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Comment: C: GATK BaseRecalibrator Step
... @ATpoint Thank you for the replies. I understand the issue and I am feeling hopeless. Is there any way at all without remapping? Any tool I can use. As of this moment I don't even know which contig in Reference == which contig in Features. ...
written 11 weeks ago by Seigfried70
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Comment: C: GATK BaseRecalibrator Step
... So when the error says that the feature contigs are different features contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_K ...
written 11 weeks ago by Seigfried70
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GATK BaseRecalibrator Step
... Hello I have been struggling with GATK 4 and feeling an acute lack of the command line pipelines available in previous versions. I took a look at the Tool Index and tried to make out the commands available from the https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels/blob/master/gatk ...
gatk written 11 weeks ago by Seigfried70
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Comment: C: Qcov Vs QcovHSP
... Trying to post here Query Sequence pIdent eValue Qcov QCovHSP Qlen K00361R:231:H5KJJBBXY:5:1105:20405:25527 Reference_DB 86.667 0.22 70 9 151 K00361R:231:H5KJJBBXY:5:1105:20405:25527 Reference_DB 90 0.78 70 7 151 K00361R:231:H5KJJBBXY:5:1105:20405:25527 Reference_DB 78.947 2.8 70 11 ...
written 3 months ago by Seigfried70
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Qcov Vs QcovHSP
... I thought I understood the difference between Qcovs and Qcovhsp I have a "reference" sequence 100bp long. I converted it into a custom blast database Reference_DB. So this database contains only 1 fasta sequence. I ran BLAST using this command blastn -db Reference_DB -query Query.fa -out Que ...
blast written 3 months ago by Seigfried70 • updated 3 months ago by Chirag Parsania1.8k

Latest awards to Seigfried

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Heatmap.2 giving specific color to a value and start gradient after
Popular Question 3 months ago, created a question with more than 1,000 views. For Quake Error Corrector
Popular Question 6 months ago, created a question with more than 1,000 views. For Finding zebrafish promoters ENSEMBL
Great Question 20 months ago, created a question with more than 5,000 views. For Heatmap.2 giving specific color to a value and start gradient after
Popular Question 20 months ago, created a question with more than 1,000 views. For Heatmap.2 giving specific color to a value and start gradient after
Scholar 22 months ago, created an answer that has been accepted. For A: Getting a distinct set of Gene Ontology terms
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Heatmap.2 giving specific color to a value and start gradient after
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How do i assign a kmer value?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Quake Error Corrector
Popular Question 2.4 years ago, created a question with more than 1,000 views. For R merge columns in the same file with identical column names and remove duplicates
Popular Question 3.0 years ago, created a question with more than 1,000 views. For ChIP-Seq TSS Line Plot

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