Tweet
Thank you!! That worked!!
-
-
Hi, I've just downloaded CONTRA_2.04 and I'm tryng to run the Test sample, but I get this error:
python contra.py --target 0247401_D_BED_20090724_hg19_MERGED.bed --test P0667T_GATKrealigned_duplicates_marked.bam --control P0667N_GATKrealigned_duplicates_marked.bam --fasta human_g1k_v37.fasta --outFolder contraTest
target : 0247401_D_BED_20090724_hg19_MERGED.bed
test : P0667T_GATKrealigned_duplicates_marked.bam
control : P0667N_GATKrealigned_duplicates_marked.bam
fasta : human_g1k_v37.fasta
outfolder : contraTest/
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
Creating Output Folder : Done.
Traceback (most recent call last):
File "contra.py", line 574, in <module>
main()
File "contra.py", line 519, in main
get_genome(params.TEST, genomeFile)
File "/home/brusel/CONTRA.v2.0.4/scripts/get_chr_length.py", line 31, in get_genome
raw_header = subprocess.Popen(args, stdout = subprocess.PIPE).communicate()[0]
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
What's happening?
Thanks
AleComment
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment