Moderator: cpad0112

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cpad011211k
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Posts by cpad0112

<prev • 1,894 results • page 1 of 190 • next >
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Comment: C: Running mutltiple Fastq files with Hisat2 in a loop
... $ ls *.gz test_1.fastq.gz test_2.fastq.gz -- for f in `ls *.fastq.gz | sed 's/_[12].fastq.gz//g' | sort -u` do echo "hisat2 -x /mnt/z/NathanHaffordTear/RNAseqproject/RNAseqanalysis/hg38_index -1 ${f}_1.fastq.gz -2 ${f}_2.fastq.gz | samtools sort -o ${f}.hisat.sorted.bam" ...
written 18 days ago by cpad011211k
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Comment: C: edgeR : How to test differential exon usage on case/control study across all tim
... try Dexseq (Inference of differential exon usage in RNA-Seq) package in R. https://bioconductor.org/packages/release/bioc/html/DEXSeq.html. With edgeR, you can use diffsplice function (https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/diffSpliceDGE) ...
written 19 days ago by cpad011211k
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Comment: C: How to extract a sequence from a multi-fasta file based on its position?
... with sed and grep (assuming that fasta is linearized) with OP fasta: $ sed -n '1~2p' test.fa | sed -n 3p | grep -A 1 -f - test.fa >org2 TATAA ...
written 7 weeks ago by cpad011211k
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Comment: C: Using awk or sed to edit a column in a gtf file
... another awk solution: $ awk -v OFS="\t" -F "\t" '{sub("^[a-zA-Z]+\.","",$2)}1' test.txt $ awk -v OFS="\t" -F "\t" '{$2=substr($2,6)}1' test.txt Pepper1.55ch01 CA01g00010 63209 63880 with gawk installed: $ awk -v OFS="\t" -F "\t" '{sub("^[a-zA-Z]{4}.","",$2)}1' test.txt ...
written 7 weeks ago by cpad011211k
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Comment: C: SNP annotation with R and SnpEff
... No. It doesn't depend on the genome/multiple adds to the dbSNP database. Calculated effect is dependent on the gene and number of transcripts at the SNP position. Multiple effects for a single gene is expected if the gene has multiple transcripts and/or the position has overlapping genes. @ https:// ...
written 7 weeks ago by cpad011211k
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Comment: C: Arrange multiple column into a single column using R-language
... with op data: > library(tidyr) > df=read.csv("test.txt", strip.white = T, stringsAsFactors = F, sep="\t", header = F) > df V1 V2 V3 V4 V5 1 1828 79595 219479 90102 1009 2 5936 114882 57685 6621 80823 3 27102 160335 51599 118987 NA ...
written 9 weeks ago by cpad011211k
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Comment: C: Fasta to FastQ with known qualities
... with [seqkit][1] and join: $ join -1 1 -2 1 -t $'\t' <(seqkit fx2tab test.fa) <(seqkit fx2tab test.fq) -o 2.1,1.2,2.3 | seqkit tab2fx output: @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 GGGTGATGGCCGCTGCCGATGGCGaaaaaaaaaaaa + IIIIIIIIIIIIIIIIIIIIIIIII ...
written 9 weeks ago by cpad011211k
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Comment: C: miRNA predictions from large set of long non coding RNA
... try mirdeep2 workflow https://www.biostars.org/u/34711/ ...
written 9 weeks ago by cpad011211k
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Comment: C: Looking for experienced bioinformatician: Ahmedabad, Gujarat, India
... https://supratechlabs.com/careers/ is loading very slow as of 19th May. Could you please look into it? @ https://www.biostars.org/u/26377/ ...
written 9 weeks ago by cpad011211k
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Comment: C: How to install tcl/tk in R in linux without root permission
... you can try brew or conda in user space @ https://www.biostars.org/u/47722/ ...
written 9 weeks ago by cpad011211k

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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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Scholar 5 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Scholar 6 months 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 7 months ago, created a question with more than 1,000 views. For GATK variant calling for RNAseq data between groups
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 7 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps

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