User: Bioradical

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Bioradical50
Reputation:
50
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New User
Location:
United States
Last seen:
2 years, 5 months ago
Joined:
3 years, 9 months ago
Email:
r*************@gmail.com

Posts by Bioradical

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Using BBMap for ChIP-seq data
... Here is the code i've tried so far: ``` bbmap.sh ref=ref in=reads.fq outm=mapped.bam maxindel=1 ambig=random sam=1.3 minid=0.95 ``` I'm not entirely sure how to read the output statsfile to indicate the percent alignments that mapped to the genome. I have currently set `maxindel=1` as I did find t ...
written 2.5 years ago by Bioradical50
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Comment: C: Using BBMap for ChIP-seq data
... Samples are single-ended, reads are 50bp. I've currently tried including the following: ``` bbmap.sh ref=ref in=reads.fq outm=mapped.bam maxindel=1 ambig=random sam=1.3 minid=0.95 ``` I've read somewhere that the default parameters can give spurious reads, and that increasing the minid will likel ...
written 2.5 years ago by Bioradical50
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Using BBMap for ChIP-seq data
... Could anyone give me some more information on using BBMap for ChIP-seq datasets? Is it recommended? Specific parameters? The defaults seem to be suitable for RNA-seq type read mapping, but I can't find absolutely any information on parameter use for ChIP. Should I go back to Bowtie2? ...
bbmap chip-seq written 2.5 years ago by Bioradical50
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Answer: A: call differential peaks H3K27ac
... You can normalize your samples for sequencing depth using Deeptools `bamCoverage` and choosing the appropriate options. You can find differentially expressed peaks using the command line tool `diffReps`. ...
written 2.8 years ago by Bioradical50
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Comment: C: How to extract bigWig signal for a given bed file?
... In bedgraph format, the fourth column is == to the signal? ...
written 2.9 years ago by Bioradical50
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How to extract bigWig signal for a given bed file?
... I'm looking for a program to extract signal values from a bigWig file for a given set of coordinates. Python, R or command line is fine (my programming is rudimentary at best). Thank you! ...
bigwig written 2.9 years ago by Bioradical50 • updated 7 months ago by chechu0860
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Comment: C: Bioinformatics project for a beginner
... NGS Analysis might be a good place to start. ChIP-Seq analysis, RNA-Seq Analysis. Go ahead and download some raw data (fastq files) from Encode or GEO. Look up a published paper and try to re-create the results. Here's a good paper on ChIP-Seq analysis: http://journals.plos.org/ploscompbiol/articl ...
written 3.7 years ago by Bioradical50
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Comment: C: How to identify a certain pattern for histone marks
... Hi Sachin,    I was looking for something similar to this and am glad I came across your program. However, I seem to be running into an issue when trying to replicate your test dataset. Here is the log: Check, if all required parameters and files are provided (Tue Dec 15 11:05:47 CST 2015).. don ...
written 3.7 years ago by Bioradical50
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Comment: C: Error when trying to use samtools to convert a sam files to a bam file
... I'm positive that the index was built for bowtie, since I used bowtie's prebuilt options. I've run bowtie before and have never run into these problems so I have no idea what's wrong. I went ahead and redid everything using the different syntax, and redownloaded the prebuilt index, and using one pro ...
written 3.7 years ago by Bioradical50
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Comment: C: Error when trying to use samtools to convert a sam files to a bam file
... Sorry, I am aware that the files are different because I attempted to re-do the bowtie and then sam to bam conversion again. Both files had these same errors. So they must both be failing at the bowtie step. Let me try your suggestions (the syntax might definitely be a problem since I'm simply follo ...
written 3.7 years ago by Bioradical50

Latest awards to Bioradical

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error when trying to use samtools to convert a sam files to a bam file
Supporter 3.7 years ago, voted at least 25 times.

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