Joining paired end reads

[Dharitri (dharitri saikia)]

Hello everyone,
I have just started working with 16s rRNA data. sequences are given in FastQ format with two files for each sample, forward and reverse. For joining these two, should I have to change the orientation or make the complementary sequence of the reverse read? Or just I have to run join_paired_ends.py with the forward and reverse fastq files in QIIME? Does QIIME have any in built tool to change the orientation or making it complementary to the forward sequence? I am really confused with this… looking forward for your kind support.

[colinbrislawn (Colin J Brislawn)]

Hello Dharitri,

Great question! All the qiime scripts should work with your reads in the same format you received them from the sequencing company. You should be able to import your data without worrying about changing their orientation.

If you are just getting started, going through the Moving Pictures tutorial is really helpful for understanding how Qiime work. Once you have it working with this example data, you can start working with your own.

@Dharitri

sequences are given in FastQ format with two files for each sample, forward and reverse.

You could use the fastq manifest format to import your data into qiime 2, or the qiime 1 script multiple_split_libraries_fastq.py.

Let me know if you have any questions,
Colin

[Nicholas_Bokulich]

@colinbrislawn

If you are just getting started, going through the Moving Pictures tutorial is really helpful for understanding how Qiime work. Once you have it working with this example data, you can start working with your own.

@Dharitri — moving pictures would be the best tutorial to help orient you, but then check out the Atacama tutorial which gives an actual example of paired-end read analysis.

[Dharitri (dharitri saikia)]

Thank you so much.This is really helpful.thanks

[Dharitri (dharitri saikia)]

Thank you so much. Atacama and moving picture tutorial are really helpful