Hi,
I am using STAR for read alignment. The STAR genome index was built on .gtf and .fa downloaded from UCSC genome browser.
Should I run rsem-prepare-reference on the same .gtf and .fa files ?
When I run the rsem-prepare-reference
I get Warning: 85 transcripts are failed to extract because their chromosome sequences are absent
Should I ignore this msg, as the transcripts look unimportant ?
Warning: Cannot extract transcript NM_023052_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_023052_5's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_023052_6's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199959_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199959_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199960_1's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199960_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199961_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_033616's sequence since the chromosome it locates, chr1_GL456221_random, is absent! Warning: Cannot extract transcript NM_001033326's sequence since the chromosome it locates, chr4_GL456216_random, is absent! Warning: Cannot extract transcript NM_001122668_1's sequence since the chromosome it locates, chr5_GL456354_random, is absent! Warning: Cannot extract transcript NM_001085530's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193668's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001193668_1's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193668_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_5's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_6's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001099348's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001099348_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001164046_1's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001164046_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199962's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199963_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199963_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001177580's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001031622_2's sequence since the chromosome it locates, chr5_JH584298_random, is absent! Warning: Cannot extract transcript NM_001031622_3's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_4's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_5's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_6's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001200055_2's sequence since the chromosome it locates, chr5_JH584298_random, is absent! Warning: Cannot extract transcript NM_001200055_3's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001200055_4's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001193667_1's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001100596's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001100596_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001270431_3's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001270360's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001270360_1's sequence since the chromosome it locates, chr4_GL456350_random, is absent!
Hi, I am using STAR for read alignment. The STAR genome index was built on .gtf and .fa downloaded from UCSC genome browser.
Should I run rsem-prepare-reference on the same .gtf and .fa files ?
When I run the rsem-prepare-reference
I get
Warning: 85 transcripts are failed to extract because their chromosome sequences are absentShould I ignore this msg, as the transcripts look unimportant ?
Warning: Cannot extract transcript NM_023052_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_023052_5's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_023052_6's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199959_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199959_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199960_1's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199960_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199961_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_033616's sequence since the chromosome it locates, chr1_GL456221_random, is absent! Warning: Cannot extract transcript NM_001033326's sequence since the chromosome it locates, chr4_GL456216_random, is absent! Warning: Cannot extract transcript NM_001122668_1's sequence since the chromosome it locates, chr5_GL456354_random, is absent! Warning: Cannot extract transcript NM_001085530's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193668's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001193668_1's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193668_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_4's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_5's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001193666_6's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001099348's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001099348_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001164046_1's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001164046_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001199962's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199963_2's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001199963_3's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001177580's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001031622_2's sequence since the chromosome it locates, chr5_JH584298_random, is absent! Warning: Cannot extract transcript NM_001031622_3's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_4's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_5's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001031622_6's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001200055_2's sequence since the chromosome it locates, chr5_JH584298_random, is absent! Warning: Cannot extract transcript NM_001200055_3's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001200055_4's sequence since the chromosome it locates, chr5_JH584299_random, is absent! Warning: Cannot extract transcript NM_001193667_1's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001100596's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001100596_2's sequence since the chromosome it locates, chr4_JH584294_random, is absent! Warning: Cannot extract transcript NM_001270431_3's sequence since the chromosome it locates, chr4_GL456350_random, is absent! Warning: Cannot extract transcript NM_001270360's sequence since the chromosome it locates, chr4_JH584293_random, is absent! Warning: Cannot extract transcript NM_001270360_1's sequence since the chromosome it locates, chr4_GL456350_random, is absent!