Hi all,
I was wondering, how does bowtie fit in with tophat. What I have done so far is the following through Galaxy-Project.
1) Converted an NGS (RNA-Seq) SRA data to FASTQ file via DRA-SRA or through EBI's SRA to FASTQ converter.
2) Uploaded this FASTQ file onto Galaxy-Project
3) Used FASTQ Groomer
4) Then used FASTQ Groomed file from part 3 with Tophat to get the accepted hits bam file, etc
5) Now based on the workflow that I am following the methods goes back to Groomed FASTQ to do bowtie
but the tophat file and bowtie file never get worked together to make one bam file...
As my ultimate goal is get expression data via cufflinks, how do the two BAM files from bowtie and tophat get incorporated together?
I have been following this: https://main.g2.bx.psu.edu/u/fluidig...naseq-workflow
and
this https://main.g2.bx.psu.edu/u/jeremy/...lysis-exercise
The second one just uses tophat. But shouldn't we index the file via bowtie as well?
If we are just using Tophat, then what purpose does bowtie have then? Because I have read in journals that we should use bowtie and tophat together.
I am confused. If someone could kindly clarify this, I would really appreciate it.
Thank you.
Zapages
I was wondering, how does bowtie fit in with tophat. What I have done so far is the following through Galaxy-Project.
1) Converted an NGS (RNA-Seq) SRA data to FASTQ file via DRA-SRA or through EBI's SRA to FASTQ converter.
2) Uploaded this FASTQ file onto Galaxy-Project
3) Used FASTQ Groomer
4) Then used FASTQ Groomed file from part 3 with Tophat to get the accepted hits bam file, etc
5) Now based on the workflow that I am following the methods goes back to Groomed FASTQ to do bowtie
but the tophat file and bowtie file never get worked together to make one bam file...
As my ultimate goal is get expression data via cufflinks, how do the two BAM files from bowtie and tophat get incorporated together?
I have been following this: https://main.g2.bx.psu.edu/u/fluidig...naseq-workflow
and
this https://main.g2.bx.psu.edu/u/jeremy/...lysis-exercise
The second one just uses tophat. But shouldn't we index the file via bowtie as well?
If we are just using Tophat, then what purpose does bowtie have then? Because I have read in journals that we should use bowtie and tophat together.
I am confused. If someone could kindly clarify this, I would really appreciate it.
Thank you.
Zapages
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