User: cpad0112

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cpad011210k
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Posts by cpad0112

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Comment: C: Pipelines and pseudocodes
... Refer to tips and tricks on trimming ngs data online. ...
written 6 hours ago by cpad011210k
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Comment: C: How to extract uniquely mapped reads in Bowtie2
... Try: samtools view -F 2304 relevant samflags: not primary alignment (0x100) supplementary alignment (0x800) ...
written 1 day ago by cpad011210k
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... try reinstalling affy library and see if the issue goes away. ...
written 1 day ago by cpad011210k
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Comment: C: Too many contig after genome assembly with Spades
... not fastq, it is fastg (updated the post). Spades outputs contigs for each kmer. With higher Kmer, contig number goes down. But the relevancy of such assembly is in question. For that reason, you may need to use software like bandage or quast/ICARUS to identify the relevant assembly ...
written 1 day ago by cpad011210k
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Comment: C: Too many contig after genome assembly with Spades
... did you have a look at fastg files and the number of contigs for each kmer? You can also check how good your assembly with Bandage https://github.com/rrwick/Bandage. https://www.biostars.org/u/27586/ ...
written 1 day ago by cpad011210k
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Comment: C: Too many contig after genome assembly with Spades
... It seems you have used several k-mer sizes. Is the contig number same across all the K-mer sizes? https://www.biostars.org/u/27586/ ...
written 1 day ago by cpad011210k
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Comment: C: Keep special character in a .txt file
... with awk and sed: $ sed -nr '/CHROM|mis|\tsyn/p' test.txt CHROM_POS ANN Annotation CM009840.1_4421500 A|missense_variant|MODERATE|LOC102415844|gene14 |1/1|c.298C>T|p.Ar|| missense CM009840.1_4421553 A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p || misse ...
written 1 day ago by cpad011210k
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Comment: C: Showing up and down regulated GO and pathway using enrichR and ggplot2
... This tutorial is very useful https://www.biostars.org/u/27586/, however code and image need revisiting. ...
written 1 day ago by cpad011210k
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Comment: C: EnhancedVolcano questions on parameters, arguments can set
... Could you provide example data for your query? ...
written 1 day ago by cpad011210k
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Comment: C: How long is the waiting time for a job to run?
... .tabular file is a tab separated values (.txt). Take a back up of .tabular file, change the extension of existing file to .tsv or .txt and then try opening with excel. One has option to change the output while using featurecounts using `-o output.txt`. I guess you are in windows, try using softwar ...
written 1 day ago by cpad011210k

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Scholar 6 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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 8 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 8 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 8 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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