I have problem to split a paired-end FASTQ dataset into two separate datasets.
In order to explain the problem clearly, I list the detail of what I did with
my dataset:
Step 1) My aim is to compare datasets for the differential alternative
splicing. I downloaded paired-end datasets at FASTQ format from SRA of NCBI as
original data.
Below is part of my paired-end FASTQ dataset that I downloaed from SRA of NCBI,
Does this dataset look OK?
@SRR192532.1.1 HWI-EAS269:1:4:655:110.1 length=35
GTTTTCTGAGTGAGAAAAGGTGTGTTTGGAGTTTG
+SRR192532.1.1 HWI-EAS269:1:4:655:110.1 length=35
I28II;II*2/<5:++,(..*943F@I.('+.35'
@SRR192532.1.2 HWI-EAS269:1:4:655:110.2 length=35
AAAGATGTTAGTGTTTTATACGGAAAGGATATCTC
+SRR192532.1.2 HWI-EAS269:1:4:655:110.2 length=35
9+*9+7@?F1206,IGI+D122&/0++-.>+6/@?
Step 2) Then I performed FASTQ groomer at setting as follows:
a) Input FASTQ quality scores type: Illumina 1.3-1.7
b)Advanced Options: Hide Advanced Options.
Did I choose the right setting for FASTQ groomer? Should I use Advanced
Options? If yes, what is the setting for Advances Options?
Below is part of groomed dataset:
@SRR192532.1.1 HWI-EAS269:1:4:655:110.1 length=35
GTTTTCTGAGTGAGAAAAGGTGTGTTTGGAGTTTG
+SRR192532.1.1 HWI-EAS269:1:4:655:110.1 length=35
*!!**!**!!!!!!!!!!!!!!!!'!*!!!!!!!!
@SRR192532.1.2 HWI-EAS269:1:4:655:110.2 length=35
AAAGATGTTAGTGTTTTATACGGAAAGGATATCTC
+SRR192532.1.2 HWI-EAS269:1:4:655:110.2 length=35
!!!!!!!!'!!!!!*(*!%!!!!!!!!!!!!!!!!
Does the groomed data look right? Is number represnting the member of a pair
correct? Here they are ".1" and ".2", should they be "/1" and "/2"?
Step 3) Then I ran FASTQ splitter with the groomed files. There is not setting
for the splitter. I chose the right groomed file and then click "Excute". Below
is the description of the splitted dataset:
empty
format: fastqsanger, database:hg19
Info: Split 0 of 15277248 reads (0.00%).
Please help me dela with this problem.
Thanks.
Jianguang Du
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