User: mike-zx

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mike-zx140
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Posts by mike-zx

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How to efficiently fetch methylation beta values across multiple genes for multiple samples?
... I wish to obtain the methylation beta values across all genes from normal tissue (colon, blood, etc.) samples in a text file of some sort. I've never worked with expression/methylation data before and I'm unsure on how to do this efficiently. So far I've looked into this database: http://mgrc.kribb. ...
mehtylation database written 8 weeks ago by mike-zx140
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Download tissue distribution data from COSMIC?
... I'm interested in having the data shown in the screenshot I include in this post in a text file of some sort, but can't seem to find a way to automatically download it from `COSMIC`; I'm interested more than anything in the mutation frequencies shown in the %mutated column. An example of the table I ...
cosmic database written 6 months ago by mike-zx140 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: basic command in bash
... I don't think this is that simple, if you wanted to do it by yourself using bash scripting you would need to do something like the following: - Print the read header and its corresponding AT% in a new file. - Given an AT% threshold or range, keep only the headers of the reads you want - Grep for th ...
written 10 months ago by mike-zx140
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Answer: A: blastp download option with csv
... Hello, if you are talking about the `HitTable.csv` file you are correct it comes with no headers, however if you download the hit table in `.txt` format you will get a file that has the description of the headers and the same information as the csv file: # Fields: query acc.ver, subject acc.ver ...
written 10 months ago by mike-zx140
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Comment: C: Extract sequences from the raw reads
... Is there any particular reason why you don't want to assemble the reads first? ...
written 10 months ago by mike-zx140
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Answer: A: counting number of genes located on positive or negative strands
... Here is a bash solution as well: #First lets define a couple of variables to act as counters for each strand ( + & - ) forward=0 reverse=0 #Now we create a loop with your lines of interest from the gff3 file as the changing variable for line in $(cat file.gff3 | grep '.*g ...
written 10 months ago by mike-zx140
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Answer: A: need code for sorting fasta header
... This gives me the exact output you want as long as `(mitochondrion)` is present in all lines: cat old_fasta_headers | sed '/^[[:space:]]*$/d' | cut -d\( -f1 | sed 's/\(\.[[:digit:]]*\) /\1\t/g ; s/$/\n/g' \ > new_fasta_headers Hope this helps. ...
written 11 months ago by mike-zx140
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Answer: A: How to separate mixed orientation raw illumina sequence into forward and reverse
... I am a little bit confused since the example lines you posted seem to be the correct expected output in fastq from a normal pair-end illumina run (all of your sequence headers in R1 are 1:N:0 and all in R2 are 2:N:0) meaning forward reads are correctly placed in R1 and reverse reads in R2. However i ...
written 11 months ago by mike-zx140
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Comment: C: Faster way to get sequences from large fasta files?
... obviously to make the "file_with_headers_list" you would: cat fasta | grep \> > file_with_headers_list ...
written 11 months ago by mike-zx140
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Answer: A: Faster way to get sequences from large fasta files?
... if you only need all the sequences without headers you could: cat fasta | paste - - | cut -f2 > output if you need each sequence in a separate file with the fasta header you could: for id in $(cat file_with_headers_list) do filename=$(cat test | grep "$id" | cut -d\> -f2) ...
written 11 months ago by mike-zx140

Latest awards to mike-zx

Scholar 9 months ago, created an answer that has been accepted. For A: manipulating a file by R or bash?
Scholar 11 months ago, created an answer that has been accepted. For A: manipulating a file by R or bash?
Scholar 11 months ago, created an answer that has been accepted. For A: manipulating a file by R or bash?
Scholar 11 months ago, created an answer that has been accepted. For A: manipulating a file by R or bash?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: manipulating a file by R or bash?

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