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Merging fastq files of the same sample across multiple flowcells

I need help finding a way to merge fastq files from multiple flowcells. I do not have access to a linux server, so the traditional answer to my problem is out. I have some experience coding with Python but it's been a while. I need a way to merge run1_ID001_R1.fastq with run2_ID001_R1.fastq, and so on and so forth. Any help would be appreciated. Thank you!

fastq merge
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updated by Ram Ram • written by lipgloss2black • lipgloss2black

"I do not have access to a linux server". So, what is your environment ?

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written by Pierre Lindenbaum Pierre Lindenbaum

install cygwin. and concatenate your fastqs using a "traditional answer"

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

every operating system has the copy method that can also concatenate files. Here is how you do it with MS-DOS ;-):

COPY [/A | /B] source [/A | /B] [+ source [/A | /B] [+ ...]] [destination] [/A | /B]] [/V] [/Y | /-Y]

To append files, specify a single file for destination, but multiple files for source (using wildcards or file1+file2+file3 format).

Source: http://www.computerhope.com/copyhlp.htm

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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