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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 4 months ago by adeena_hassan40
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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 9 months ago by adeena_hassan40 • updated 9 months ago by h.mon26k
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Comment: C: how can find exlusively expressed genes between two genomes
... Thank you for correction and useful information. :) ...
written 20 months ago by adeena_hassan40

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