gravatar for sarai

7 hours ago by

Hi everyone!

I'm new on RNA-Seq analysis and I need your help. I'm trying to merge the transcript.gtf files I got with cufflinks but when I write the following command I get an error.

Can anyone suggest me how to solve this?

Thanks so much!

cuffmerge -g Mus_musculus.GRCm38.101.gtf.gz -s Mus_musculus.GRCm38.dna.primary_assembly.fa.gz assemblies.txt

[Sat Dec  5 20:19:09 2020] Beginning transcriptome assembly merge
-------------------------------------------

[Sat Dec  5 20:19:09 2020] Preparing output location ./merged_asm/
Traceback (most recent call last):
  File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 580, in <module>
    sys.exit(main())
  File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 546, in main
    chrom_info = get_gtf_chrom_info(gtf, chrom_info)
  File "/home/msmenfig/tools/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 476, in get_gtf_chrom_info
    left = int(cols[3])
ValueError: invalid literal for int() with base 10: '9x11x9ei;xb6}xf6xcex08xbex90x8d;xf8x95x8bSxb5xa6xb3qxb7xf6xccxeax1fOxcfx9fO_9xa9xaa2?x18Xxe4{xa5x97x1dxa3rRRx9a>x93Hxcex82xe3x1b;x12xcfxee)x99xb7`Cx9f+x95[7x18x94x8fxe1?0xc3.fxa6x90xa5Wxf8x15x8axcb]~Ex90x0cxcdx07x0fsxbcJx9dlxc8xd1x82x8cxd9JNdxacx0cx05[xb6kxabx1c"xe3xb2x1803`x07Mx86$2xb6ix866rWxf0WFx9dx05xa7xc4xd8x8bnPx8exe1xc7x1a|x08%Vxf74xe9'

link

modified 7 hours ago

by

_r_am31k

written
7 hours ago
by

sarai0



Source link