User: 3335098459

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333509845920
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Posts by 3335098459

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Recombination location in gubbins output
... Hi, I think you should try PHANDANGO. There are many examples shown according to your demand. ...
written 16 days ago by 333509845920
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Extract start and stop codons in multiple seq alignment
... Hi, I have multiple sequence alignment files and each contains around 450 sequences. I have been looking for software that extracts start and stop codon with sequence ID. Most of the questions in this and other websites were focused on deleting stop codons or extracting stop codon from one sequence ...
gene sequence alignment written 21 days ago by 333509845920 • updated 21 days ago by Pyretu10
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GWAS analysis with truncated gene phenotype
... Hi, I have performed a pangenome analysis on NCBI downloaded genome and found various strains with a specific truncated gene(s) that will surely result in a change in phenotype. Lets say if we consider the phenotype a beginning point and perform a GWAS analysis (to find out other affected genes) ...
gene genome snp written 27 days ago by 333509845920
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Comment: C: awk, copy and paste single line command
... Thanks for pointing out the possible solution. I have used the following command to solve this problem. (sed '1d' penicilin_SNPs.txt | cut -d "_" -f 2, 4) | awk '{}' > example.txt I also did some manual changes and it worked. ...
written 27 days ago by 333509845920 • updated 4 days ago by Kevin Blighe51k
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Comment: C: bedtools and SNPs for pyseer-GWAS analysis
... Actually there was some issue with the bedtools/bcftools compiling code and installation. Previous wrapper tool also used bedtools for indexing and compression. While re-indexing I figured out this point and I used different tool to combine, compress and indexing. Also thanks for explaining the bgzi ...
written 29 days ago by 333509845920
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Comment: C: awk, copy and paste single line command
... Yes you are right. This is the complete command divided into different sections by \\ I guess. cat <(echo "#CHR SNP BP minLOG10(P) log10(p) r^2") \\\ <(paste <(sed '1d' penicillin_SNPs.txt | cut -d "_" -f 2) \\\ <(sed '1d' penicillin_SNPs.txt | cut -f 4) | \\\ ...
written 29 days ago by 333509845920 • updated 29 days ago by genomax74k
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Comment: C: awk, copy and paste single line command
... Thanks but removing these \\ solved the last two errors but the errors related to cat and paste are still there Cat: / dev / FD / 63: no file or directory Cat: / dev / FD / 62: no file or directory Paste: / dev / FD / 62: no file or directory how can I solve these? ...
written 29 days ago by 333509845920
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Comment: C: bedtools and SNPs for pyseer-GWAS analysis
... After your reply, I have used other packages to generate indexed vcf file. vcfcombine *.vcf > merged.vcf (I guess there was some issue with bedtools) bgzip -c merged.vcf > snps.vcf.gz tabix -p vcf snps.vcf.gz Thanks for pointing out the direction. ...
written 29 days ago by 333509845920
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awk, copy and paste single line command
... Hi I am just a beginner in the command line and newly introduced to Linux. I am using software that suggested the following command to convert all the coordinates to plot. cat <(echo "#CHR SNP BP minLOG10(P) log10(p) r^2") \\ <(paste <(sed '1d' penicillin_SNPs.txt | cut -d "_" -f 2) ...
software error written 29 days ago by 333509845920 • updated 5 days ago by Biostar ♦♦ 20
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bedtools and SNPs for pyseer-GWAS analysis
... Hi I have used snippy package for SNP calling and later on used those for pyseer-GWAS analyses. But it seems that this command of bedtools cannot read the vcf files. bcftools merge -m none -0 -O z *.vcf.gz > merged.vcf.gz I am getting this error: bcftools: Relink /root/min ...
genome gene snp written 4 weeks ago by 333509845920 • updated 4 weeks ago by ATpoint26k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Read, concatenate and merge the multiple fasta sequence files in R
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