Comments (5)
Hi Yuyang,
I'll take a look at your error as soon as possible.
For an example .3dg
file, there's already a FTP link in README.md; but it's not showing up because GitHub doesn't support FTP links. Here I've pasted it below for your convenience:
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3271nnn/GSM3271352/suppl/GSM3271352_gm12878_06.impute3.round4.clean.3dg.txt.gz
The corresponding GEO accession contains final files like this for all single cells, as well as all intermediate files starting from raw.con.gz
. However, the two earliest files, aln.bam
and phased.seg.gz
haven't been provided because of their large size.
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Your error seems to come from a discrepancy in chromosome naming between your genome file (chr1
in your hg19.fa
) and the SNP file you used (1
in snps/NA12878.txt.gz
). You must change one of them to match the other.
The importance of chromosome name matching has been mentioned in an earlier comment for this repo, and another comment for the companion repo hickit.
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from dip-c.
Hi Tan,
I run the dip-c seg command and got the issues:
The messages is as following:
Traceback (most recent call last):
File "/THL8/home/liubin/software/dip-c-master/dip-c", line 130, in
main()
File "/THL8/home/liubin/software/dip-c-master/dip-c", line 42, in main
return_value = seg.seg(sys.argv[1:])
File "/THL8/home/liubin/software/dip-c-master/seg.py", line 115, in seg
seg_data.clean()
File "/THL8/home/liubin/software/dip-c-master/classes.py", line 204, in clean
for name in self.reads.keys():
RuntimeError: dictionary changed size during iteration
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Hi @liubinnk1, please see my reply to your identical question in the other thread.
Best,
Tan
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Related Issues (20)
- SNP HOT 2
- hickit: invalid option -- 'M' HOT 2
- Is variant masked genome ref required for the alignment ? HOT 2
- About single cell chromatin A/B compartment clustering HOT 4
- How to remove the abnomal copy-number (CN) gains or losses regions HOT 4
- Question about SNP file HOT 2
- The coordinate system of SNP file. HOT 2
- How to generate cpg.1m.txt file for GRCh38? HOT 2
- Quality control of DipC data
- How to install Dip-C?
- distances to the nuclear center
- remove repetitive (contact-less) regions encountered a problem HOT 2
- 'str' error when convert 3dg file to cif file HOT 1
- Generating 3D proximity map and visualization of TAD
- Discrepancy in txt file names between 2018 and 2019 publications
- Calculating radius of a given nucleus
- Can not colored HOT 4
- Haploid data
- Error: generate the 3D structure HOT 4
- On the issue of duplicated chromosomes
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