Hi,
I am quite new to NGS analysis.
I came to know about ugene recently while searching command free best NGS analysis tools running on windows.
I have 6 RNA seq data retrieved from one thousand plant transcriptome database. (https://sites.google.com/a/ualberta.ca/onekp/).
Download from: https://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/oneKP_capstone_2019/transcript_assemblies
These are:
Sample 1:
PAWA-SOAPdenovo-Trans-assembly.fa
UDUT-SOAPdenovo-Trans-assembly.fa
UVDC-SOAPdenovo-Trans-assembly.fa
Sample 2:
WTKZ-SOAPdenovo-Trans-assembly.fa
WXVX-SOAPdenovo-Trans-assembly.fa
ZHMB-SOAPdenovo-Trans-assembly.fa
I was trying RNA seq analysis with tuxedo tool.
I am not able to select bowtie index file under tophi setting. The reference genome is Arabidopsis_thaliana_Ensembl_TAIR10. Which file to be selected under Bowtie index folder, and what to be given under Bowtie index base name.
Under cufflinks setting, which file to be selected under reference annotation and RABT annotation, mask file.
Under cuffmerge setting, which file to be selected under reference annotation and reference sequence.
Under cuffdiff setting, which file to be selected under Flag bias correct.
Error:
The error was to set TopHat, Cufflinks, Cuffcompare, cuffmerge, Cuffdiff. I downloaded the external tools and tried to set but failed to set it.
I read the ugene manual to set all the issue, but failed.
I shall be very much thankful if someone guide me to resolve the issues.
I shall be obliged forever.
Ali