Gtf file with NCBI Ids for backlocate

[pawarad]

This is a follow-up question on #170 issue. I am able to operate backlocate successfully after you provided the correct gtf file. Thank you so much for solving the issue promptly. I request you to help me with my following questions.

1) The gtf file contains ensembl IDs. Can you please provide link to a gtf file which contains NCBI Ids? I tried downloading from UCSC browser but that gtf file doesn't work.

2) Do you have command in backlocate where we can provide a list of input instead a single input? Thank you.

[lindenb]

The gtf file contains ensembl IDs. Can you please provide link to a gtf file which contains NCBI Ids?

no, I don't know such file.

Do you have command in backlocate where we can provide a list of input instead a single input?

cat input.txt | java -jar backlocate.jar

[lindenb]

see https://stackoverflow.com/a/49206830/58082

[vkulaganathan]

I tried using a list, but I get the[INFO][Launcher]backlocate Exited with failure (-1) error

$ cat input_list.txt | java -jar dist/backlocate.jar -R hg19.fa --gtf Homo_sapiens.GRCh37.87.gtf

#User.Gene  AA1 petide.pos.1    AA2 transcript.name transcript.id   transcript.strand   transcript.AA   index0.in.rna   wild.codon  potential.var.codons    base.in.rna chromosomeindex0.in.genomic exon    messages    extra.user.data
[SEVERE][Launcher]Expected 2 tokens, but got 1
 * [1]  "ICOS\tF141X"

[INFO][Launcher]backlocate Exited with failure (-1)

Didn't generate results. What am I doing wrong? The input_list.txt contains the following: ICOS\tF141X CDH10\tL614X KCNE2\tV49X MMP24\tV603X

[lindenb]

\t should be tabulations, NOT a litteral \ followed by t... of course...