Question: Pair end alignment using HISAT2
0
gravatar for premraj.preeti
20 days ago by
premraj.preeti10 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
ADD COMMENTlink modified 16 days ago by sudheendrar10 • written 20 days ago by premraj.preeti10
1
gravatar for Jennifer Hillman Jackson
16 days ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 16 days ago by Jennifer Hillman Jackson25k

Thanks Jennifer that was very helpful.

ADD REPLYlink written 13 days ago by premraj.preeti10
1
gravatar for sudheendrar
16 days ago by
sudheendrar10
sudheendrar10 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 COMMENTlink written 16 days ago by sudheendrar10

Thanks , this was very informative

ADD REPLYlink written 13 days ago by premraj.preeti10
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