CUFFLINKS error: Warning: invalid start coordinate at line:
1
0
Entering edit mode
2.9 years ago

I downloaded a ChIP-seq dataset from ENCODE (ENCFF615OUG.bam) and made an indexed bam file of it (ENCFF615OUG.bai), then extracted the chromosome 22 sequence (chr22.bam) using samtools view

samtools view -b ENCFF615OUG.bam chr22 > chr22.bam

I need to get FPKM values for genes in chr22, so I tried running CUFFLINKS using the GTF file for chromosome 22 from UCSC table browser

cufflinks -G grch38-chr22.gtf chr22.bam

However when I run this command it outputs the following

[10:28:21] Loading reference annotation.
Warning: invalid start coordinate at line:
666 ENST00000615943.1   chr22   -   10736170    10736283    10736170    10736170    110736170,  10736283,   0   U2  none    none    -1,
Warning: invalid start coordinate at line:
668 ENST00000618365.1   chr22   -   10936022    10936161    10936022    10936022    110936022,  10936161,   0   CU459211.1  none    none    -1,
Warning: invalid start coordinate at line:
669 ENST00000623473.1   chr22   -   11065973    11067346    11065973    11067346    211065973,11067334, 11066015,11067346,  0   CU104787.1  incmpl  incmpl  0,0,
Error parsing strand (1) from GFF line:
669 ENST00000624155.1   chr22   +   11066500    11068089    11066500    11068089    211066500,11067984, 11066515,11068089,  0   BAGE5   cmpl    cmpl    0,0,

I'm not sure what causes these errors. I downloaded the gtf file right from UCSC Table so I'm not sure what to do to fix this error. Any ideas?

ChIP-Seq • 1.0k views
ADD COMMENT
0
Entering edit mode

Can you show reads aligned from your bam ?

ADD REPLY
0
Entering edit mode
2.9 years ago

I discovered my problem. When downloading from the UCSC table browser I did not select GTF file output

ADD COMMENT
0
Entering edit mode

Problem completely solved, then? If 'yes', I will move this to an answer.

ADD REPLY
0
Entering edit mode

Yes, problem is solved

ADD REPLY

Login before adding your answer.

Traffic: 2656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6