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Moderator: cpad0112

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cpad0112 ♦ 10k
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Posts by cpad0112

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Comment: C: How can I view and manage the Trinity.fasta by bash
... try using tools like [seqkit][1]: [1]: https://bioinf.shenwei.me/seqkit/download/ ...
written 5 days ago by cpad0112 ♦ 10k
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Answer: C: how to extract per base information (in coverage track of IGV) from .bam file
... 1. Download IGVtools from here: https://software.broadinstitute.org/software/igv/download 2. Extract IGVtools in folder of your choice 3. sh //igvtools count -w 1 --bases input.bam output.wig hg38 wig file is tsv file. reference: https://digibio.blogspot.com/2014/07/calculate-coverage-from- ...
written 6 days ago by cpad0112 ♦ 10k
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Comment: C: Create snakefile based on R script
... From https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html: > the syntax follows that of S4 classes with attributes that are R > lists, e.g. we can access the first input file with > snakemake@input[[1]] (note that the first file does not have index 0 > here, because R start ...
written 7 days ago by cpad0112 ♦ 10k
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Comment: C: Passing a file to sed to remove all lines that match +1 in file B from file A
... safer way using [seqkit][1]: seqkit grep -v -f input.fasta [1]: https://bioinf.shenwei.me/seqkit/download/ ...
written 7 days ago by cpad0112 ♦ 10k
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Answer: C: Create a 3-D PCA
... try rgl package in R. Refer to this page as well: http://www.sthda.com/english/wiki/scatterplot3d-3d-graphics-r-software-and-data-visualization https://www.biostars.org/u/44687/ ...
written 10 days ago by cpad0112 ♦ 10k
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Comment: C: Help with RNA-seq analysis
... Try BRB array tools to analyze RNAseq data in excel https://www.biostars.org/u/51383/. link to brbarray tools: https://brb.nci.nih.gov/BRB-ArrayTools/Documentation.html ...
written 10 days ago by cpad0112 ♦ 10k
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Answer: A: Find bams with identical names and merge them
... $ ls test1/*.bam test1/bam1.bam test1/bam2.bam test1/bam3.bam test1/bam4.bam test1/bam8.bam $ ls test2/*.bam test2/bam1.bam test2/bam2.bam test2/bam3.bam test2/bam4.bam test2/bam5.bam $ find test1 test2 -type f -name '*.bam' | xargs basename -a | sort | uniq -d| par ...
written 10 days ago by cpad0112 ♦ 10k
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Comment: C: how to extract coding sequences (CDS) from a bam file or vcf file ?
... If you have reference fasta and corresponding annotation file with CDS and vcf, you can use getfasta from bedtools suite, to get CDS sequence. You can also use bcftools consensus function to get sequence information using VCF. samtools or bamutils can help you in extracting regions of interest fro ...
written 10 days ago by cpad0112 ♦ 10k
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Comment: C: RNA-seq Data Excel Formatting
... two ways: 1. Vlookup function in excel 2. Load excel sheets in msaccess, write SQL ...
written 10 days ago by cpad0112 ♦ 10k
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Comment: C: Designing a primer from reads
... isn't this in principle looking for "ATCGATCG" motif as all the previous bases can be any base? If so, you would have lots of amplification. @ https://www.biostars.org/u/47631/ ...
written 12 days ago by cpad0112 ♦ 10k

Latest awards to cpad0112

Scholar 7 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 7 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Appreciated 8 days ago, created a post with more than 5 votes. For A: How to make a clear box plot or whatever beautiful for showing the ratio of two
Scholar 28 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Popular Question 6 weeks ago, created a question with more than 1,000 views. For GATK variant calling for RNAseq data between groups
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 7 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 9 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 9 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 10 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 10 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Appreciated 3 months ago, created a post with more than 5 votes. For C: can someone read this result to me
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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