yezhengSTAT
commented
4 years ago Hello! May I know how did you download the data from GEO? Sometimes when you download a paired-ended sequencing data and split into two end fastq files, a suffix such as "-1" or "_1" may be appended to the read name to indicate this is end 1. In our case, we don't want this to happen and the read name should be exactly the same and in the same order.
The corresponding python codes to check the read name is as below, if they are not exactly the same, you will see the error message.
if r1.qname == r2.qname:
if r1.is_unmapped == True and r2.is_unmapped == True:
unmapped_count += 1
continue
elif r1.is_unmapped == False and r2.is_unmapped == False:
mapped_count += 1
if is_uniread(r1) == True and is_uniread(r2) == True:
uni_count += 1
(r1, r2) = sam_flag(r1, r2, readEnd1, readEnd2)
outfile.write(r1)
outfile.write(r2)
else:
singleton_count += 1
else:
print("Read id in read 1 and read 2 file does not match. Please check the input read files and sort them correctly.")
sys.exit()Otherwise......may I see a fraction of your input fastq files?
Thanks, Ye
suyeonwy
Hi, I'm using FreeHiC for simulating Cow Hi-C data.
For fastqFile data using during training steps, SRR6691720 data (https://www.ncbi.nlm.nih.gov/sra/?term=SRR6691720) was used and other parameters are below.
train=1 simulate=1 postProcess=1 coreN=20 mismatchN=3 gapN=1 mismatchP="" gapP="" chimericP="" simuN=157702285 readLen=80 resolution=40000 lowerBound=80000 refragU=800 ligateSite="AAGCTAGCTT"
After simulating Hi-C data, I checked the output of the simulation and found that read IDs in each read file did not match. Also, the numbers of reads in read 1 and read 2 files are different. There was a warning message in log but I already checked that my input FASTQ files do not have any problems. (All reads are sorted equally in both input read files and all IDs are matched)
Read id in read 1 and read 2 file does not match. Please check the input read files and sort them correctly.Could you tell me how to fix this problem?