User: evafinegan

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evafinegan0
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Posts by evafinegan

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Comment: C: linear mixed model for gene expression data in R
... Thank you! I do not want to do differential expression analysis. I want to run a linear mixed model to generate a value for each gene as shown in my original question. ...
written 4 days ago by evafinegan0
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Comment: C: linear mixed model for gene expression data in R
... Thank you! Is it better than `lme4` package? ...
written 4 days ago by evafinegan0
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linear mixed model for gene expression data in R
... I have gene expression data for multiple genotypes as FPKM matrix: gene Sample1 Sample2 Sample3 gene A 19.6 13.5 16.7 gene B 17.8 19.7 14.3 In the matrix, genes are in rows, columns have samples with FPKM values for each gene across the samples. I want to run a line ...
R written 5 days ago by evafinegan0
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Comment: C: how to convert a txt file to bed file
... This works: `perl -pe "s/:/\t/; s/-(\d+)$/\t\1/"` Thank you! ...
written 10 days ago by evafinegan0
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Comment: C: how to convert a txt file to bed file
... Using this the output is: S_12g0010.2.1 0 S_12g0030.2.1 0 S_12g0040.2.1 0 S_12g0080.2.1 0 S_12g0020.2.1 0 S_12g0000.1-c2.1 0 Now there is no third column, ...
written 10 days ago by evafinegan0
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Comment: C: how to convert a txt file to bed file
... Yes, I have used the same command that you suggested. So my input text file has some of the lines like this: S_12g0010.2.1:0-170 S_12g0030.2.1:0-476 S_12g0040.2.1:0-94 S_12g0080.2.1:0-259 S_12g0020.2.1:0-382 S_12g0000.1-c2.1:0-210 Your suggestion works well for rest of ...
written 10 days ago by evafinegan0
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Comment: C: how to convert a txt file to bed file
... Thank you, I have used your suggestion. It made a bed file but I see some strange things in some of the lines: S_12g00500.1.1 0 273 S_12g0000.1 c2.1 0-210 I think the second line should look like this: S_12g0000.1c2.1 0 210 The original line in txt file looks like this: S_12g0 ...
written 10 days ago by evafinegan0
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how to convert a txt file to bed file
... Hello, I have a text file and I want to convert it to a bed file. My text file looks like: S_12g0010.2.1:0-170 S_12g0030.2.1:0-476 S_12g0040.2.1:0-94 S_12g0080.2.1:0-259 S_12g0020.2.1:0-382 Can anyone suggest a way for this conversion. Thank you! ...
next-gen written 10 days ago by evafinegan0 • updated 10 days ago by JC11k
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freebayes not reading the chunks of regions file
... Hello, I am using freebayes for SNP calling using: RUN=${SLURM_ARRAY_TASK_ID} INPUT_DIR=/path/ OUTPUT_DIR=/path/ INPUT=$(ls $INPUT_DIR/*.txt | sed -n ${RUN}p) SAMPLE=$(basename "$INPUT" .txt) freebayes -f genome.fasta \ -L list_of_bam.txt \ ...
snp written 12 days ago by evafinegan0
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Comment: C: freebayes error for SNP calling
... Thank you, here is what I got for one of bam files which were pointed out in the error: samtools flagstat sample35.bam 32008143 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 567823 + 0 supplementary 8427353 + 0 duplicates 29096062 + 0 mapped (90.90% : N/A) ...
written 13 days ago by evafinegan0

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