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Question: Pair end alignment using HISAT2
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gravatar for premraj.preeti
20 days ago by
premraj.preeti • 10
premraj.preeti • 10 wrote:

Hi,

I have a FASTQ file that is a paired library. I want to align this FASTq file to Hg19 genome.

After the selecting the genome reference genome , I have selected Is this a single or paired library, option as paired library.

Now I need to provide 2 FastQ file. Can I provide the same FastQ file. I am confused.

Please help.

Regards, Preeti
rna-seq galaxy hisat2 • 74 views
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modified 16 days ago by sudheendrar • 10 • written 20 days ago by premraj.preeti • 10
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gravatar for Jennifer Hillman Jackson
16 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If the forward and reverse reads are interleaved/interlaced in the same dataset, you'll need to split it into two distinct fastq datasets. One containing the forward reads, the other with the reverse.

Some tools accept interleaved fastq data but most do not.

https://galaxyproject.org/support

Thanks! Jen, Galaxy team
ADD COMMENT • link written 16 days ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jennifer that was very helpful.

ADD REPLY • link written 13 days ago by premraj.preeti • 10
1
gravatar for sudheendrar
16 days ago by
sudheendrar • 10
sudheendrar • 10 wrote:

Hi Preeti, Once you import your FASTQ file to Galaxy, have a look at it by clicking on the eye icon. If you see both reads (e.g if its illumina, then it would be /1 and /2 ), then your reads are interleaved. HISAT2 alignment program can take this data as it is. you do not have to split FASTQ into two files (one forward and one reverse). In HISAT2 settings, select "Paired End Data from Single Interleaved dataset" under the option "Is this a single or paired library". If your reference genome is not available, just upload it to Galaxy using GetData/Fetch pasting the FTP link. Follow this link for more info https://biostar.usegalaxy.org/p/24822/
ADD COMMENT • link written 16 days ago by sudheendrar • 10

Thanks , this was very informative

ADD REPLY • link written 13 days ago by premraj.preeti • 10
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