User: anikcropscience
anikcropscience • 40
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Posts by anikcropscience
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... That is great. I have not tried snakemake yet. But it seems very useful for reproducible research. Thank you. ...
written 5 days ago by
anikcropscience • 40
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... Oh great. I will run it. See if it works. Thanks a lot. ...
written 6 days ago by
anikcropscience • 40
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... Thank you very much. That is awesome! ...
written 6 days ago by
anikcropscience • 40
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... Hello,
I have a folder containing *.fastq.gz files (R1 and R2) for many samples. For example, in the folder "Raw_WGS", I have several files like
> Sample_1_R1.fastq.gz, Sample_1_R2.fastq.gz, Sample_2_R1.fastq.gz,
> Sample_2_R2.fastq.gz, Sample_3_R1.fastq.gz, Sample_3_R2.fastq.gz
I have anot ...
written 6 days ago by
anikcropscience • 40
• updated
6 days ago by
Jeremy Leipzig ♦ 19k
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... I have tried this withs snps/all. But still showing the same output. ...
written 22 days ago by
anikcropscience • 40
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... I saw this post and used the --remove-duplicates command. But it is not working at all. ...
written 22 days ago by
anikcropscience • 40
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... Hello,
I have a VCF file containing ~900K SNPs. There are some tri-allelic SNPs in the dataset. So, I used bcftools to split those tri-allelic SNPs into biallelic SNPs. Then I tried to remove the duplicated SNP IDs that were generated after splitting the tri-allelic SNPs. I used bcftools as well bu ...
written 22 days ago by
anikcropscience • 40
• updated
22 days ago by
Kevin Blighe ♦ 71k
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... Can someone please provide me some useful tutorial links to perform linkage disequilibrium analysis? I have some significant SNPs from a GWAS study. Now, I want to do LD analysis and create an LD-heatmap using the r-square values. But struggling a bit with how to start.
Some tutorials based on HapM ...
written 8 weeks ago by
anikcropscience • 40
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... Hello, thank you for your elaborate answer. Yes, it worked perfectly. I did not have any problems while running the code or manipulating the graphic features. I highly appreciate all your efforts into this.
Thank you very much.
For now, the ROI options is not necessary at all for my paper. But in ...
written 9 weeks ago by
anikcropscience • 40
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... Yes, the sequence is 1944 bp long. The problem is, I have SNP in multiple positions so if I need to zoom in then I would have to do it multiple times in the same figure, which is not what I want in a publication. And the figure is going to be included in a manuscript (I will surely cite your GitHub ...
written 9 weeks ago by
anikcropscience • 40
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