User: evafinegan

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evafinegan0
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Posts by evafinegan

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Comment: C: error in sed usage
... `INPUT_FILE` is expected to give each of the `bed` file name along with path to run with an array. ...
written 2 days ago by evafinegan0
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Comment: C: error in sed usage
... `RUN` represents 10 `bed` files; `INPUT_DIR` represents path to `bed` files; `OUTPUT_DIR` represents path for `vcf` files to be made ...
written 2 days ago by evafinegan0
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Comment: C: error in sed usage
... I have added the code that I used it for. Please let me know if it is works now or not. Thank you! ...
written 2 days ago by evafinegan0
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error in sed usage
... Hello, I am using this loop for a software" RUN=$(printf "%02d" ${SLURM_ARRAY}) INPUT_DIR=/path OUTPUT_DIR=/path echo "RUN" INPUT_FILE=$(ls $INPUT_DIR/*.bed | sed -n ${RUN}p) SAMPLE=$(basename "$INPUT_FILE" .bed) echo "RUN #${RUN} with sample ${SAMPLE}" freebayes -f ...
sequencing written 2 days ago by evafinegan0
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Comment: C: conversion of gff to bed file
... I used: gff2bed < sample.gff > sample.bed cut -f 1-4 sample.bed > sample_1.bed awk 'BEGIN {FS="\t"; OFS=","} {print $4, $1, $2, $3}' sample_1.bed > sample_2.bed ...
written 16 days ago by evafinegan0
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how to manage missing data in vcf file
... Hello, I have a multi sample vcf file made by using freebayes: freebayes -f transcripts.fasta \ -L list.txt \ --targets bed.list > out.vcf I have not used any filtering steps and I found that only ~10% of total SNPs are observed in more than half of the sampl ...
snp written 4 weeks ago by evafinegan0
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eQTL analysis using BGData in R
... Hello, I have two datafiles, 1. gene expression matrix with genes in rows and samples in columns with respective FPKM values, and 2. SNP data (vcf file). I want to do `eQTL` analysis using `BGData` package in `R`. I could not find any beginner tutorial about the same package on how to prepare the ...
R written 6 weeks ago by evafinegan0
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Comment: C: converting vcf into simpler version for downstream analysis
... I have added the information, thank you! ...
written 8 weeks ago by evafinegan0
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converting vcf into simpler version for downstream analysis
... Hello, I have made a multi sample vcf file using freebayes. I want to use it for downstream association analysis. I have calls like: 0/0:37:37,0:37:1499:0:0:0,-11.1381,-135.125 ./.:.:.:.:.:.:.:. I was wondering whether I can convert these calls into simple format for eQTL analysis using BGDat ...
snp written 8 weeks ago by evafinegan0
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Blast2GO : how to select only transcription factors
... Hello, I am using Blast2Go to retrieve the GO terms for a list of genes. I used protein sequences and ran Blast. Then I ran InterPro Scan and merged the annotations. I got these parameters for each gene: GO IDs GO Names Enzyme Codes Enzyme Names InterPro IDs InterPro GO IDs InterPro GO Names ...
blast2go written 8 weeks ago by evafinegan0

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