RepeatMasker format in SQuIRE Fetch

Question

[Javier]

I have a question regarding the format of a RepeatMasker file found in the following link: https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/

I have been using SQuIRE to analyze expression data and I used the "Fetch" function to obtain the RepeatMasker from the reference hg38 human genome. Usually, this files contain 14 columns [SW, perc div, perc del, perc ins, query sequence, position in query (begin, end and left), matching repeat, repeat class/family, position in repeat (begin, end, left) and ID], but the rmsk.txt.gz file found in the link mentioned contains an additional column at the beginning.

This file has the same information as any other RepeatMasker file, with the exception of this first column containing numbers, and having the "repeat class/family" column separated in two (one column for class, another for family).

I haven't found any information regarding this first column, can anyone help me understand the information inside it?

Answer 1

[iqra]

Hi, I have encountered this problem by using squire pipeline. but this command works for pair-end data and shows this error for single-end data. before half of my jobs are done and now its shows an error. have you solve this problem?

$ squire Count -m /home/data/TE-data/Dmrt1-data/Mapping -c /home/data/TE-data/Dmrt1-data/squire_clean -o /home/data/TE-data/Dmrt1-data/counts -t /home/data/TE-data/reference -f /home/data/TE-data/reference -r 50 -n SRR1757699 -b GRCm38 -p 32

Traceback (most recent call last): File "/home/iqra/miniconda3/envs/squire_env/bin/squire", line 10, in <module> sys.exit(main()) File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 1805, in main avg_fraglength=uniquecount(unique_bedfile,RepCalc_dict,read_locdict) File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 1231, in uniquecount unique_fragavg=unique_fragsum/int(unique_linecount) ZeroDivisionError: division by zero