eXpress seems to treat soft clipping in read as indels. This can be proven with the option --max-indel-size. I have reads with soft clips ranging from 3 to 40 bases. With default --max-indel-size (i.e., 10), express could only quantify reads with max indels <= 10 includin soft clips. I lost most of my perfectly matching reads in quantification because they have soft clipped parts which are longer than 10 bases long . With changing the --max-indel-size to 40 could quantify most of the reads, but sometimes lead to segfault.
eXpress seems to treat soft clipping in read as indels. This can be proven with the option --max-indel-size. I have reads with soft clips ranging from 3 to 40 bases. With default --max-indel-size (i.e., 10), express could only quantify reads with max indels <= 10 includin soft clips. I lost most of my perfectly matching reads in quantification because they have soft clipped parts which are longer than 10 bases long . With changing the --max-indel-size to 40 could quantify most of the reads, but sometimes lead to segfault.