Moderator: cpad0112

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cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k
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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 cpad011210k

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Scholar 7 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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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
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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
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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
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