The sorted and filtered refFlat file was generated as a blank file

[ShenTTT]

I tried to detect APA sites using the following command:

for i in ls -1 *_coverage.txt | sed 's/_coverage.txt//' do echo "detect APA sites for ${i}" ./APA_sites_detection -ref refFlat.txt -cov ${i}_coverage.txt -l 150 -o ${i}_APA.txt

However, the output were all blank files. I tried to run the sample analysis and it went well. I noticed that a sorted and filtered refFlat file is always generated when the program is executed properly, but in my case, that file was generated as a blank file from my original refFlat file. I checked the format of my refFlat file and I think it perfectly matches the sample. I have attached part of my refFlat file here for your reference and I wonder how this could be solved?

gene-LOC112057652   rna-XM_024098097.1  NW_019872794.1  +   4   241 4   241 1   4,  241,
gene-LOC112057648   rna-XM_024098095.1  NW_019869963.1  -   12  523 12  523 1   12, 523,
gene-LOC112057647   rna-XM_024098094.1  NW_019869709.1  -   57  548 57  420 1   57, 548,
gene-LOC112057646   rna-XM_024098093.1  NW_019869273.1  +   8   612 8   612 1   8,  612,
gene-LOC112057645   rna-XM_024098092.1  NW_019869155.1  +   6   585 6   585 1   6,  585,
gene-LOC112057644   rna-XM_024098090.1  NW_019869143.1  -   91  589 157 555 2   91,496, 407,589,
gene-LOC112057643   rna-XM_024098089.1  NW_019868965.1  +   32  654 273 654 2   32,549, 285,654,
gene-LOC112057642   rna-XM_024098088.1  NW_019868912.1  -   4   658 4   658 1   4,  658,
gene-LOC112057641   rna-XM_024098087.1  NW_019868824.1  -   5   671 5   671 1   5,  671,
gene-LOC112057640   rna-XM_024098086.1  NW_019868816.1  +   3   672 3   672 1   3,  672,
gene-LOC112057638   rna-XM_024098085.1  NW_019868738.1  +   212 687 212 687 1   212,    687,
gene-LOC112057637   rna-XM_024098083.1  NW_019868597.1  -   12  717 12  717 1   12, 717,
gene-LOC112057636   rna-XM_024098082.1  NW_019868536.1  +   3   734 3   734 1   3,  734,
gene-LOC112057634   rna-XM_024098081.1  NW_019868163.1  +   11  761 619 761 1   11, 761,
gene-Trnav-cac-12   rna-Trnav-cac-12    NW_019868151.1  -   646 719 719 719 1   646,    719,
gene-LOC112057632   rna-XM_024098080.1  NW_019868123.1  +   8   812 138 812 1   8,  812,
gene-LOC112057631   rna-XM_024098078.1  NW_019868097.1  +   189 852 189 801 2   189,712,    627,852,
gene-LOC112057630   rna-XM_024098077.1  NW_019868075.1  -   72  832 107 807 2   72,726, 254,832,
gene-LOC112057629   rna-XM_024098076.1  NW_019867948.1  +   0   931 28  895 2   0,143,  62,931,
gene-LOC112057627   rna-XM_024098075.1  NW_019867915.1  +   57  522 57  522 1   57, 522,
gene-LOC112057626   rna-XM_024098073.1  NW_019867910.1  +   710 1553    710 1553    1   710,    1553,
gene-LOC112057625   rna-XM_024098072.1  NW_019867898.1  +   110 876 228 876 2   110,773,    362,876,
gene-LOC112057624   rna-XM_024098071.1  NW_019867745.1  -   107 856 167 856 2   107,704,    364,856,
gene-LOC112057623   rna-XM_024098070.1  NW_019867725.1  -   18  999 18  875 2   18,744, 289,999,
gene-LOC112057621   rna-XM_024098068.1  NW_019867647.1  +   3   989 3   989 1   3,  989,

[ShenTTT]

it seems that adding 'NM_' to the first two columns solved this problem

[arefeen]

Happy to know the issue is solved.

On Thu, Apr 8, 2021, 7:10 AM ShenTTT @.***> wrote:

it seems that adding 'NM_' to the first two columns solved this problem

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