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Old 04-26-2018, 10:14 PM   #1
Meyana
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Location: Japan

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Cool Add user specified reads to fastq to validate analysis method?

Hi,

I am analyzing mtDNA and am looking for indels, especially I am hoping to catch some large deletions.
I have performed 150bp PE on MiSeq using NexteraXT library prep.

Using different tools, I am not able to pick up the large deletions I was hoping, however, I am seeing a lot of small indels and substitution mutations, which I also was expecting.

To test my analysis methods, I would like to add some "in silico" generated reads to my fastq files. I am hoping to make 'reads' that cross a large deletions (i.e. the first 75bp of read1 at position 1-75 of mtDNA and the last 75bp and position 1001-1075 of mtDNA, read2 maybe something like position 1275-1201 [i.e. not split up at different genomic position]).

How would I go about manipulating my data in such a way?

I hope my question in clear...

Thanks!
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Old 05-06-2018, 03:59 PM   #2
Meyana
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Default

Anyone that might know how to do something like this?
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Old 05-16-2018, 12:26 PM   #3
dylanfofylan
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Cool

Hi Meyena,

Last year, I wrote a short python script to fabricate fastq data for validating software functions. Here's my very (very) simple implementation: https://github.com/dfox3/fabricate_f...icate_fastq.py

You provide a filename (--o) (to overwrite, not to append to), the DNA code you want to to fabricate (--i), and how many times you want to replicate it (--d).

If you're interested in running this function on a set of sequences, I'd consider expanding on it. I'll probably need to use this again in the future.

Hope you find this useful
-dylan

Last edited by dylanfofylan; 05-16-2018 at 12:34 PM. Reason: i didnt want to mislead
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