Hi Everyone,
I am doing a comparison of tophat2 vs STAR alignment of my RNA-seq data, and trimmed vs untrimmed data. (I was getting different results using tophat2 than the bioinformaticians were with STAR but they don't seem to interested in determining why which is why I am testing it out myself). I found quite a large difference in mapping efficiency in tophat when I trimmed my reads using cutadapt (up to 35% more mapping) compared to untrimmed. I know STAR is supposed to soft clip the reads but I'm still curious to see if there is any difference and the percentages compared to tophat2. While I have no problems with my raw input data in STAR, it doesn't seem to like my trimmed reads and gives the following error:
EXITING because of FATAL ERROR: Read1 and Read2 are not consistent, reached the end of the one before the other one
SOLUTION: Check you your input files: they may be corrupted
I assume this is because during the trimming process, they will no longer all be 100bp long and I will lose some reads altogether. I tried the following option: --readMatesLengthsIn NotEqual but it still gave the same error.
Any suggestions? Will STAR let me run the files if they aren't equal? Or is it pointless to test trimmed reads with STAR at all?
Thanks for your help!
I am doing a comparison of tophat2 vs STAR alignment of my RNA-seq data, and trimmed vs untrimmed data. (I was getting different results using tophat2 than the bioinformaticians were with STAR but they don't seem to interested in determining why which is why I am testing it out myself). I found quite a large difference in mapping efficiency in tophat when I trimmed my reads using cutadapt (up to 35% more mapping) compared to untrimmed. I know STAR is supposed to soft clip the reads but I'm still curious to see if there is any difference and the percentages compared to tophat2. While I have no problems with my raw input data in STAR, it doesn't seem to like my trimmed reads and gives the following error:
EXITING because of FATAL ERROR: Read1 and Read2 are not consistent, reached the end of the one before the other one
SOLUTION: Check you your input files: they may be corrupted
I assume this is because during the trimming process, they will no longer all be 100bp long and I will lose some reads altogether. I tried the following option: --readMatesLengthsIn NotEqual but it still gave the same error.
Any suggestions? Will STAR let me run the files if they aren't equal? Or is it pointless to test trimmed reads with STAR at all?
Thanks for your help!
Comment