Hi Everyone,
I am new with DeSeq and EdgeR. I have done the following:
1) Tophat2 (provided Ensembl GTF and Fasta files)
2) Used Samtools to convert the files to Sam format (offline)
3) HTseq and used the same GTF file from Tophat2. (offline)
4) Used Iplant Collaborative Join tab delimited to merge the Counts into one file. -Edited/removed no_feature, ambiguous, too_low_aQual:, not_aligned, alignment_not_unique in the output file and added Organs headers for each rep.
5) Used EdgeR and DeSeq respectively on Iplant Collaborative.
Now I was wondering how could I possibly create heat map based on the genes that I interested based on EdgeR and DeSeq. Or is there any better method to analyze these genes via EdgeR and DeSeq.
I have already used Tuxedo pipeline to create a heat map using CummeRbund for the species.
I have 2 replicates for Organ A and 2 replicates for Organ B. The p values and log information seem to indicate high values for the genes that I am interested in.
In total I hope to have 3 Heatmaps with the specific genes of interests only:
1) EdgeR
2) DeSeq
3) Tuxedo Package - Cuffdiff/CummeRbund.
If someone could kindly help me on how I could go about this. I would really appreciate it. Thank you.
I am new with DeSeq and EdgeR. I have done the following:
1) Tophat2 (provided Ensembl GTF and Fasta files)
2) Used Samtools to convert the files to Sam format (offline)
3) HTseq and used the same GTF file from Tophat2. (offline)
4) Used Iplant Collaborative Join tab delimited to merge the Counts into one file. -Edited/removed no_feature, ambiguous, too_low_aQual:, not_aligned, alignment_not_unique in the output file and added Organs headers for each rep.
5) Used EdgeR and DeSeq respectively on Iplant Collaborative.
Now I was wondering how could I possibly create heat map based on the genes that I interested based on EdgeR and DeSeq. Or is there any better method to analyze these genes via EdgeR and DeSeq.
I have already used Tuxedo pipeline to create a heat map using CummeRbund for the species.
I have 2 replicates for Organ A and 2 replicates for Organ B. The p values and log information seem to indicate high values for the genes that I am interested in.
In total I hope to have 3 Heatmaps with the specific genes of interests only:
1) EdgeR
2) DeSeq
3) Tuxedo Package - Cuffdiff/CummeRbund.
If someone could kindly help me on how I could go about this. I would really appreciate it. Thank you.
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