hi,
I use RSEM (http://deweylab.biostat.wisc.edu/rsem/README.html) to analysis my RNA-seq data and want to summarize expression level of each RefSeq ID.
the command I used is as below:
rsem-calculate-expression -p 7 --fragment-length-min 51 --fragment-length-max 51 --fragment-length-mean 51 --fragment-length-sd 0
BTW, the length of all my reads is 51bp
I found that many isoform from the same gene got quite different TPM and FPKM. An example is as below:
transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
NM_001130147.1 CCDC77 2359 2309.00 317.27 16.83 11.21 100.00
NM_001130148.1 CCDC77 2305 2255.00 2.23 0.12 0.08 100.00
as you see. NM_001130147.1 and NM_001130148.1 are different isoform of CCDC77 and the mRNA seq is quite similar with each other. but the TPM as well as FPKM is quite different which I regard it as err.
Does anyone meet the err? can you help me?
I use RSEM (http://deweylab.biostat.wisc.edu/rsem/README.html) to analysis my RNA-seq data and want to summarize expression level of each RefSeq ID.
the command I used is as below:
rsem-calculate-expression -p 7 --fragment-length-min 51 --fragment-length-max 51 --fragment-length-mean 51 --fragment-length-sd 0
BTW, the length of all my reads is 51bp
I found that many isoform from the same gene got quite different TPM and FPKM. An example is as below:
transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
NM_001130147.1 CCDC77 2359 2309.00 317.27 16.83 11.21 100.00
NM_001130148.1 CCDC77 2305 2255.00 2.23 0.12 0.08 100.00
as you see. NM_001130147.1 and NM_001130148.1 are different isoform of CCDC77 and the mRNA seq is quite similar with each other. but the TPM as well as FPKM is quite different which I regard it as err.
Does anyone meet the err? can you help me?
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