Moderator: Damian Kao
Damian Kao ♦ 15k
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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... My recommendation is to not over-optimize unless this is a personal project for learning purposes.
There are three main considerations here all related to scale:
1. How many concurrent users do you expect to be using this database?
2. Is this pre-dominantly a read-only database where users query ...
written 15 months ago by
Damian Kao ♦ 15k
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... Try setting --outFilterMatchNmin to 20 to see if you can get more mapping. However, that means it only requires 20 bases to map, which is pretty low. ...
written 17 months ago by
Damian Kao ♦ 15k
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... Technically, RPK values do not violate assumptions of TMM.
TMM is just a technique that tries to find the non-DE portion of the expression distribution by very liberally trimming off outliers. It doesn't matter what kind of expression units you are using.
However, RPK values do violate assumptio ...
written 17 months ago by
Damian Kao ♦ 15k
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Answer:
A: Trimmomatic output file Issue
... It looks like you are not specifying an output file for the -trimlog parameter. So it thinks your `output_forward_paired.fq.gz` is an input.
I hope you still can still redownload `sample1_R1_001.fastq.gz`, because it might have been overwritten. ...
written 17 months ago by
Damian Kao ♦ 15k
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... Takes in fasta file and a second parameter for homopolymer length.
It streams through each line to find homopolymers. Outputs chromosome, start, end, homopolymer base, length of homopolymer.
I tested it out on this fasta file:
>A
AGTCAAAA
GGGGTTTTCCCC
>B
AGTCCCCCTTTTAAA ...
written 17 months ago by
Damian Kao ♦ 15k
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... You have a .csv file with chromosome, start, end coordinates. You can change that into a .bed file pretty easily. Same with your SNP csv file.
Convert those csv files to bed and then use bedtools intersect. ...
written 18 months ago by
Damian Kao ♦ 15k
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... Yeah that could be it. You can check this by looking at the insert size distribution of your PE reads. See if it is smaller than 2 * average read length. The 9th column of your .sam/.bam should be the insert size. ...
written 18 months ago by
Damian Kao ♦ 15k
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... I am not sure what program you are using to generate the .vcfs. But you should look into the manual of the program and see if it outputs depths using the format fields in the vcf. For example, you have "DP" field in your vcf that shows the depth of the individual samples. Perhaps one of the other f ...
written 18 months ago by
Damian Kao ♦ 15k
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... Can you post a couple of lines of your vcf file? ...
written 18 months ago by
Damian Kao ♦ 15k
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... There is a -L flag that you can use with samtools to output alignments overlapping intervals defined by a .bed file. That's probably your best option. You'll have to convert your exons.txt to a bed file. ...
written 18 months ago by
Damian Kao ♦ 15k
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For deseq2 user defined size factors
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