Question: automating multiple fastq.gz -> SAM
0
gravatar for s.vandenhurk
4.0 years ago by
s.vandenhurk10
Netherlands
s.vandenhurk10 wrote:

Hello Guys,

I am interested in automating the combining of multiple fastq.gz files. As you can see in the image below I have already indexed my reference genome with BWA and I have combined the fastq.gz files from my COL strain. Because this Arabidopsis is a test set, I could do it manually. However, in the near future I plan to do the same thing with over 500 strains. So I would like to automate the process.

I have used the linux command cat *_1.fastq.gz > Combined_1.fastq.gz to get it to work at the COL strain. Should I create some sort of bash loop for things like this?

tree

 

I have already aligned these Combined_1 and Combined_2 to the reference genome and I have used these results with BWA sampe to get a SAM file. So far, results look promising. But, could this process also be automated? 

sequencing assembly • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum118k • written 4.0 years ago by s.vandenhurk10

How did you make that graph?

ADD REPLYlink written 22 months ago by jnowacki70

https://linux.die.net/man/1/tree

ADD REPLYlink written 22 months ago by Pierre Lindenbaum118k
1
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

See my demo project https://github.com/lindenb/ngsxml to generate Makefile-based workflows using XSLT

 

wordlow

ADD COMMENTlink written 4.0 years ago by Pierre Lindenbaum118k
1

I had considered posting a comment of the form, "Pierre's reply mentioning ngsxml in 3, 2, 1...". I guess I should have!

ADD REPLYlink written 4.0 years ago by Devon Ryan88k

:-)                          .

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k
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