####最近一段时间碰见的问题 (07252023 update)
When use STAR to do alignment work, it sometimes show the error:
“EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length
@NB551599:72:H2F7GBGXN:1:21102:1810:15491
TTATAATTATTTTAAATTCTCAGTCTGAAAATGTCAAAATTTGTGTGATATCTGAGTCT
SOLUTION: fix your fastq file”
排除问题期间的代码尝试：
grep -B4 -A8 "^@NB551599:72:H2F7GBGXN:1:21102:1810:15491" Apheresis11.fq1 （-B and -A mean upstream and downstream contents）
grep -B4 -A8 "^@NB551599:72:H2F7GBGXN:1:21102:1810:15491" Apheresis11.fq2
发现fq2文件没有对应的quality score…
[shaol2@cn1050 Apheresis11]$ wc -l Apheresis11.fq1 Apheresis11.fq2
108545568 Apheresis11.fq1
103735594 Apheresis11.fq2
(发现fq1 and fq2 reads不对等。然而在原始的local文件夹中，重新generate fq1 and fq2之后发现length of row is equal….)
所以问题应该就是在传输的过程中文件不完整导致的
