Issues with import fastq files

(Ashutosh Das) #1

Hi
I am new to QIIME 2, I am using qiime2-2019.1 on a ubuntu 18.04 virtual machin on a windows host
I have 9 fastq.gz files for 9 samples, each file has both R1 and R2 reads in the same fastq file:

@S0R0/1
CCGAATTATTAGTAACAATTCCTTTGTTACTGTTGTATCCTTTAGTATGCTTTAGTATGCTAAAGTATGTTTTCCTGAGTACAACGATATTAACATGGCTTGAAAATACATATCCTGGAATCTTTACAGAGTATTTGGAAACTTTTCCAA
+
[email protected]>KHIKKJJHKFKKEG)[email protected];EE<IKEEEBEEECEBFEAEEEEDEDEEE:=EEEEEEEDDE1;[email protected]$EF:$EGEDEA:4EE;FCDE9E
@S0R0/2
TAATGTGGAAATCAATTGTATTATACCACACCCTGCCTTAAAGTCGACCTTGATTTGGAAAAGTTTCCCAAGACTCTGTAAAAATTCAAGGATATGTATTTTCAAGTCATGTTAATATCGCTGTACTCAGGGAAACATACTTTAGCATAC
+
[email protected]=HJKKKKJKFJ=K[email protected]EEECCE6DE1FEA6$DFE:=?EEAA=BD$EEEDD,[email protected]$A?EECE9BDADE=D$DEB

I am trying to import some fastq files. I have gone through several options by reading the tutorials and suggestions for specifying the

–types and --input format for my

I am still missing the right input --type and input-format for such kind fastq files

Could you please suggest me to overcome this issue?

Thanks in advance
Ashutosh

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(Colin Brislawn) #2

Hello Ashutosh,

Welcome to Qiime 2! Thanks for posting. :qiime2:

These fastq files look like a good fit for the “fastq-manifest” format. Take a look at this:
https://docs.qiime2.org/2019.1/tutorials/importing/#fastq-manifest-formats

Let me know if that works for you. If you have any other questions, feel free to post them here along with the commands you tried and their outputs and messages.

Colin

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(Ashutosh Das) #3

Hi @colinbrislawn
Thanks for your reply
I have gone through the tutorial before, I not sure how to make the path for the forward and reverse reads since I have forward and reverse reads in the same file, how to make like following option

sample-id,absolute-filepath,direction

Lines starting with ‘#’ are ignored and can be used to create

“comments” or even “comment out” entries

sample-1,$PWD/some/filepath/sample1_R1.fastq.gz,forward
sample-2,$PWD/some/filepath/sample2_R1.fastq.gz,forward
sample-1,$PWD/some/filepath/sample1_R2.fastq.gz,reverse
sample-2,$PWD/some/filepath/sample2_R2.fastq.gz,reverse

Should I do it as a single end, but each sample id is appeared twice for R1 and R2?
then how to fix the menifest for the following files
sample_0_reads.fq.gz sample_4_reads.fq.gz sample_8_reads.fq.gz
sample_1_reads.fq.gz sample_5_reads.fq.gz sample_9_reads.fq.gz
sample_2_reads.fq.gz sample_6_reads.fq.gz
sample_3_reads.fq.gz sample_7_reads.fq.gz

Ashutosh

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(Colin Brislawn) #4

Hello Anshutosh,

Oh, I missed this! I forgot your reads were ‘interleaved.’ Thanks for reminding me. :+1:

The bad news is that interleaved fastq files are not supported yet. It looks like the Qiime 1 script extract_reads_from_interleaved_file.py could help you demultiplex this file.

Would you like to try the Qiime 1 script or try something else?

Colin

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(Ashutosh Das) #5

Thanks Colin
I would like to use Qiime 1 scripts before trying something else

Ashutosh

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