Hello everyone,

I am using DEXSeq package and I am getting an error.

First I ran the following command without any problem:

python2.7 /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_prepare_annotation.py ./Arabidopsis_thaliana.TAIR10.42.gtf ./Arabidopsis_thaliana.TAIR10.42.DEXSeq.gff

Here is how the output looks:

head -n 5 Arabidopsisthaliana.TAIR10.42.DEXSeq.gff 1 dexseqprepareannotation.py aggregategene 3631 5899 . + . geneid "geneAT1G01010" 1 dexseqprepareannotation.py exonicpart 3631 3913 . + . transcripts "transcript:AT1G01010.1"; exonicpartnumber "001"; geneid "geneAT1G01010" 1 dexseqprepareannotation.py exonicpart 3996 4276 . + . transcripts "transcript:AT1G01010.1"; exonicpartnumber "002"; geneid "geneAT1G01010" 1 dexseqprepareannotation.py exonicpart 4486 4605 . + . transcripts "transcript:AT1G01010.1"; exonicpartnumber "003"; geneid "geneAT1G01010" 1 dexseqprepareannotation.py exonicpart 4706 5095 . + . transcripts "transcript:AT1G01010.1"; exonicpartnumber "004"; geneid "geneAT1G01010"

Then I tried:

python2.7 /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py -p yes -r name -a 10 -s no -f bam ./S01_mapped_sorted.bam ./S02_mapped_sorted.bam  ./Arabidopsis_thaliana.TAIR10.42.DEXSeq.gff > S01_S02_dexseq_count

And I got the following error:

Traceback (most recent call last): File "/usr/local/lib/R/site-library/DEXSeq/pythonscripts/dexseqcount.py", line 94, in <module> for f in HTSeq.GFFReader( gfffile ): File "/usr/lib/python2.7/dist-packages/HTSeq/init.py", line 207, in iter strand, frame, attributeStr ) = line.split( "\t", 8 ) ValueError: need more than 4 values to unpack

Any help will be appreciated, Thanks.

Paola

In your call to dexseq_count.py, you should first give the name of the GFF file, and only after that list the BAM files.

So, it should be

python2.7 /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py -p yes -r name -a 10 -s no -f bam ./Arabidopsis_thaliana.TAIR10.42.DEXSeq.gff ./S01_mapped_sorted.bam ./S02_mapped_sorted.bam  > S01_S02_dexseq_count