User: adeena_hassan

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Posts by adeena_hassan

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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... Thank you so much. Its helpful. You made my day! ...
written 16 months ago by adeena_hassan50
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... yeah, there are lines with with contig information. I skipped them earlier because of the header length. bcfftools already installed. Version: 0.1.19-96b5f2294a Thank you so much for response! ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ...
written 16 months ago by adeena_hassan50
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... yes, i have the corresponding vcf files of all three samples. It is one file per sample. Following are the headers of one file ##fileformat=VCFv4.1 ##ALT= ##ALT= ##FILTER= ##FILTER= 200.0 || ReadPosRankSum < -20.0"> ##FILTER= 60.0 || MQ < 40.0 || MQRankSum < ...
written 16 months ago by adeena_hassan50
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... Hi finswimmer , Human genome was used as a reference genome and I have the corresponding vcf file (Filtered_Variants.vcf) , bam file and fastq files. Could u guide now? ...
written 16 months ago by adeena_hassan50
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... This will extract all the HET positions but I need only those HET positions in parents that are HOM in child. ...
written 16 months ago by adeena_hassan50
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... I hve a little bit understanding of perl language. Is this csv module work with perl ? And is there any possible command-line solution in linux ?? ...
written 16 months ago by adeena_hassan50
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how to filter 3 variants files (in excel format) simultaneously?
... Assalam o Alaikum Everyone! I have 3 annotated variants list files (excel files) of three patients from same family (2 parents 1 child). I want to extract the positions that are **Hetro** in parents and **Homo** in child. For example: SNP_Indel_1.xlsx (Parent) #CHROM POS REF ALT DP AD QUAL ...
perl commandline snp whole exome sequencing written 16 months ago by adeena_hassan50
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Comment: C: Error in Calculation of Ka/Ks value using Ka/Ks calculator
... @katerinapargana Ka/Ks calculator only worked for pairs of sequence and it worked well with the input given above. Before calculation, gaps and stop codons between compared sequences will be removed. ...
written 16 months ago by adeena_hassan50
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Comment: C: Error in Calculation of Ka/Ks value using Ka/Ks calculator
... Ka/Ks calculator is a command line tool and it takes input in AXT format. A perl script that convert FASTA file into AXT is available with the tool. It reads a pair of sequences and computes corresponding estimates (length of the two sequence must b equal). Here is my input file in AXT format: ...
written 20 months ago by adeena_hassan50 • updated 20 months ago by h.mon29k
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Comment: C: how can find exlusively expressed genes between two genomes
... Thank you for correction and useful information. :) ...
written 2.7 years ago by adeena_hassan50

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