User: kk.mahsa

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kk.mahsa40
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Posts by kk.mahsa

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Convert repeat masked out file to bed file format
... i have two RepeatMasker .out files (homology_based and de novo identification of repeats). i want to combine these files to obtain a final file but i do not know how do it. following workflow can help me? 1. converting two RepeatMasker to bed using rmsk2bed 2. use bedtools intersect 3. converting ...
written 8 days ago by kk.mahsa40
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Comment: C: how to combine two output of RepeatMasker?
... example file is here [example][1] [1]: https://ufile.io/u5d6p ...
written 11 days ago by kk.mahsa40
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Comment: C: how to combine two output of RepeatMasker?
... i have two output files (.out) that some elements between them are shared and some are unique. i want to get one file that give me consensus repetitive elements ...
written 11 days ago by kk.mahsa40
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how to combine two output of RepeatMasker?
... hi i run homology-based and denovo identification of repeats using Repeatmasker and Repeatmodeler. Now i have two output that i want to combine them to obtain final content of different repetitive elements. how can i do it? anyone can to help me? ...
repeats next-gen repeatmasker written 11 days ago by kk.mahsa40
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Comment: C: extraction homozygous SNPs for first individual when second individual has no SN
... i installed your program but there is not vcffilterjdk.jar file in dist folder. thare are three files including: vcffilterjs.jar, annotproc.jar and vcffilterjs. so i try: vcf-merge input_1.vcf input_2.vcf > merged.vcf java -jar dist/vcffilterjs.jar -e 'return variant.getGenotype(0).isHomVar() ...
written 18 days ago by kk.mahsa40
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Comment: C: extraction homozygous SNPs for first individual when second individual has no SN
... thanks for your quick answer dear Pierre, i think my question is not clear. i have two vcf file and my goal is extraction Homozygous snps for first vcf file when second vcf file has no snp (hom or het) in that position. ...
written 19 days ago by kk.mahsa40
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extraction homozygous SNPs for first individual when second individual has no SNPs in same position
... hi how i can extract homozygous SNPs for first individual (vcf file) when second individual has no SNPs in the same position? thanks in advance ...
homozygous snp written 19 days ago by kk.mahsa40 • updated 19 days ago by Pierre Lindenbaum96k
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Comment: C: how can i remove duplicated variants from vcf file?
... thank you capd0112, i used bcftools norm and it worked. ...
written 26 days ago by kk.mahsa40
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Comment: C: how can i remove duplicated variants from vcf file?
... your answer was really helpfull, thank you so much Pierre. it worked ...
written 26 days ago by kk.mahsa40
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Comment: C: how can i remove duplicated variants from vcf file?
... thanks Pierre for your answer, i ran your cammand and get an vcf file as output but when used bcftools stats i got this error. Failed to open output.vcf: unknown file type why bcftools can not regognize output as a vcf file? i need to output file for downstream analysis as vcf file ...
written 26 days ago by kk.mahsa40

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