guoyanzhao
commented
6 years ago Hi Sapsanas, It's likely file format. You said works correct for test data. Did you compare the test input and the actual input and see what's the difference?
the script get sequence IDs and extract sequences for those read IDs from the file ".RepeatMasker.goodSeq.masked.fa". Did you check that file whether the format is correct? or maybe check output file after step 1 and 2 to see whether at the initial steps the correct format was generated Guoyan
On Monday, June 11, 2018, 5:29:23 AM CDT, Sapsanas <notifications@github.com> wrote: Hello!
I faced with the following problem: applying of Unmasked_seq_to_masked_seq.pl at 12th step gives incorrect output #4: ${SAMPLE_ID}.RepeatMasker.goodSeq.RefGenome.unmapped.masked.fasta, it contains only reads IDs, not sequences themselves. All other output files of this step seem to be correct. Additionally, Unmasked_seq_to_masked_seq.pl works correct for test data. Have you ever met this problem? Is there any possibility to solve it?
Thank you in advance!
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Sapsanas
Hello!
I faced with the following problem: applying of Unmasked_seq_to_masked_seq.pl at 12th step gives incorrect output #4: ${SAMPLE_ID}.RepeatMasker.goodSeq.RefGenome.unmapped.masked.fasta, it contains only reads IDs, not sequences themselves. All other output files of this step seem to be correct. Additionally, Unmasked_seq_to_masked_seq.pl works correct for test data. Have you ever met this problem? Is there any possibility to solve it?
Thank you in advance!