User: Cookie-san

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Cookie-san0
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Posts by Cookie-san

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Comment: A: The Biostar Handbook. A bioinformatics e-book for beginners.
... Hi! I am 5 months into analyzing NGS data and I would like to purchase this book.I'm not sure how advanced it is though. I have a Master's degree in Bioinformatics but my course majorly focused on Structural Biology. So I can't really say I'm new to this field but I certainly only started working i ...
written 17 days ago by Cookie-san0
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Comment: C: bcftools mpileup --max depth : What would be a reasonable setting for this optio
... The default is 250 and the manual suggests to increase it. > Check the bcftools mpileup --max-depth option, most likely it should be increased. Note that by default only 250 reads per-file are considered at a position! The previous samtools mpileup default was 8000. Hence I wanted to know wha ...
written 17 days ago by Cookie-san0
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Comment: C: best women crossfit shoes
... Is this post even allowed on this site? ...
written 17 days ago by Cookie-san0
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bcftools mpileup --max depth : What would be a reasonable setting for this option?
... Hello! I am trying to extract the consensus sequence from a sorted BAM file that was got after alignment. The commands I will be using are: bcftools mpileup -Ou -f Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa AEB21A.bam | bcftools call -mv -Ob -o AEB21A_calls.bcf bcftools index AEB21A_call ...
consensus bcftools mpileup written 17 days ago by Cookie-san0
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Comment: C: Error using feature counts with DESeq2 : Cannot create DESeqData object
... Hey, thank you SO MUCH for asking me to check the dimensions of my data frame. I was indeed missing around 8000 genes. I figured out the error; I was using this code to make my Gene_IDs unique and convert them to row names: readcounts <- aggregate(readcounts[-1],readcounts[1],mean) row.n ...
written 27 days ago by Cookie-san0
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Comment: C: Error using feature counts with DESeq2 : Cannot create DESeqData object
... Ah sorry XP New to R. Edit: Sorry it worked. Should I convert the integer object back to a data frame? Again, sorry if the question is too obvious. readcounts <- as.integer(as.matrix(readcounts)) head(readcounts) 4422 3 1063 164 5193 654 DESeq.ds <- DESeqDataSetFromMatrix(c ...
written 28 days ago by Cookie-san0
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Comment: C: Error using feature counts with DESeq2 : Cannot create DESeqData object
... The file was given to me by my professor as a csv file. Yes these are raw counts. I imported the file using the ```read.table``` command. ```as.integer(readcounts)``` doesn't work because ```readcounts``` is a dataframe. head(readcounts) C11 C15 C19 C23 N11 N15 N19 N23 NM_000014 4422 ...
written 28 days ago by Cookie-san0
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Error using feature counts with DESeq2 : Cannot create DESeqData object
... I have a file of read counts with which I want to find the differentially expressed genes from using DeSeq2. The file was generated using feature counts. C11 C15 C19 C23 N11 N15 N19 N23 NM_000014 4422 14216 8885 17031 8162 4811 12536 8273 NM_000015 3 0 7 2 0 9 2 6 ...
deseq2 featurecounts rna-seq written 28 days ago by Cookie-san0 • updated 9 days ago by Biostar ♦♦ 20
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Comment: C: BQSR vs VQSR
... Yes, specifically to calculate the QD or Quality-by-depth value. ...
written 4 weeks ago by Cookie-san0
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Comment: C: What is the importance of checking per base sequence content and per sequence GC
... Wow that's news to me. Thanks! ...
written 4 weeks ago by Cookie-san0

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