Hi all,
I have just started using TopHat and it runs successfully and most of the results make sense. However, when I load the coverage.wig into UCSC (and also when I look at the coverage.wig file by hand) there are some lines that have negative values in the last column, which I thought contained some approximation of the number of reads-- so a negative value doesn't have a logical meaning. This only happens in ~1000 lines of the .wig file, so it is a relatively rare occurrence, but it creates long stretches of consecutive negative values. One thought I had was this was their way of displaying opposite strand transcription, but there's no documentation that explains this and looking at my data that doesn't really make sense. Just wondering if anyone else has experienced this or understands what it means. Also, my accepted_hits.sam file is not sorted, which made me worry maybe the program didn't run completely. Is it true that it is supposed to be sorted in the output?
Many thanks.
I have just started using TopHat and it runs successfully and most of the results make sense. However, when I load the coverage.wig into UCSC (and also when I look at the coverage.wig file by hand) there are some lines that have negative values in the last column, which I thought contained some approximation of the number of reads-- so a negative value doesn't have a logical meaning. This only happens in ~1000 lines of the .wig file, so it is a relatively rare occurrence, but it creates long stretches of consecutive negative values. One thought I had was this was their way of displaying opposite strand transcription, but there's no documentation that explains this and looking at my data that doesn't really make sense. Just wondering if anyone else has experienced this or understands what it means. Also, my accepted_hits.sam file is not sorted, which made me worry maybe the program didn't run completely. Is it true that it is supposed to be sorted in the output?
Many thanks.
