Whether hg19.fa.out.bed is needed be change?

[GAOwy123]

Whether hg19.fa.out.bed is needed be change? When I run the cscMap, I got follow error. Error: unable to open file or unable to determine types for file /thinker/storage/user/gaowy2/pipline/cscMap/hg19.fa.out.bed

• Please ensure that your file is TAB delimited (e.g., cat -t FILE).
• Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED). Error: unable to open file or unable to determine types for file /thinker/storage/user/gaowy2/pipline/cscMap/hg19.fa.out.bed

So, I check the hg19.fa.out.bed. head hg19.fa.out.bed SW perc perc perc query position in query matching repeat position in repeat score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID

1504 1.3 0.4 1.3 chr1 10001 10468 (249240153) + (CCCTAA)n Simple_repeat 1 463 (0) 1 3612 11.4 27.0 1.3 chr1 10469 11447 (249239174) C TAR1 Satellite/telo (399) 1712 483 2 437 23.5 18.6 3.5 chr1 11504 11675 (249238946) C L1MC LINE/L1 (2236) 5646 5449 3 239 29.4 1.9 1.0 chr1 11678 11780 (249238841) C MER5B DNA/hAT-Charlie (74) 104 1 4 318 23.0 3.8 0.0 chr1 15265 15355 (249235266) C MIR3 SINE/MIR (119) 143 49 5 203 16.2 0.0 0.0 chr1 16713 16749 (249233872) + (TGG)n Simple_repeat 1 37 (0) 6 239 33.8 14.8 0.0 chr1 18907 19048 (249231573) + L2a LINE/L2 2942 3104 (322) 7

[wyt14]

Make sure it's a bed file format! thx~

[fanch1122]

@wyt14 Can you give a sample file of hg19.fa.out.bed awk 'NR >3 {print $5"\t"$6"\t"$7"\t"$10"\t"$1"\t"$9"\t"$6"\t"$7} ' <(cat oxy.out) | sed $'s/\tC\t/\t-\t/g' > repeatmasker.oxy.bed

this my rule of adjust .out file to bed,I’m not sure this is right for cscMap.