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发表于 2022-9-22 09:37:23
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查看: 1238 |
回复: 0
背景
近期做的RNA-Seq数据上游,hisat2+stringtie流程,使用的stringtie官方的prepDE.py脚本定量。
- prepDE.py -i sample_lst.txt
复制代码 命令报错:
- Error: could not locate transcript ENST00000624361 entry for sample Sample10
- Traceback (most recent call last):
- File "/share/home/xiehs/tools/stringtie-2.1.4.Linux_x86_64/prepDE.py", line 281, in <module>
- geneDict.setdefault(geneIDs<i>,{}) #gene_id
- KeyError: 'ENST00000624361'</i>
复制代码
解决方案
经过一系列的google探索,得出了这是因为前面使用的stringtie版本不对,下面贴出官方的回答:
- Thank you so much @Gin-Wang I took a look at the data you uploaded and I can confirm now that the problem is real and correctly reported by users in this thread (and in #234), stringtie 2.0 with the -e option outputs a few STRG entries which should NOT be there, as the output should only contain the MSTRG entries that were given in the -G file.
- We will fix this -e problem soon and report back here, until then please use stringtie v1.3.6 for quantification via prepDE (for short reads there shouldn't be a significant difference).
复制代码 意思就是选用1.3.6的版本,他们会尽快修复。
那么如何快速的切换版本呢?自然是使用conda管理。
- conda activate test
- conda install stringtie=1.3.6-0
复制代码 使用我们就用绝对路径写命令即可。
- /share/Software/miniconda3/envs/test/bin/stringtie
复制代码 跑完gtf文件,用脚本定量,果然没有报错了。
特此分享给大家。
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