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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
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The mapped reference id NC_000067.7 from file mice_miRNA_reads_vs_GRCm39_Trim4.arf is not an id of the genome file /home/genome/GCA_GRCm39.fa #121

Closed genesio-Ka closed 1 week ago

genesio-Ka commented 3 months ago

I was successful mapping mice miRNA sequence reads using Mapper.pl after installing bowtie 1.2.3 to read bowtie-2 indexes

However, I was not successful in quantifying the expression levels using mirDeep2.pl. This is the script i used: ./miRDeep2.pl mice_miRNA_reads_Trim4.fa /home/genome/GCA_GRCm39.fa mice_miRNA_reads_vs_GRCm39_Trim4.arf /home/mirbase/mmu_22_mature_true.fa /home/mirbase/all_22_mature_true.fa /home/mirbase/mmu_22_hairpin_true.fa -t mice 2 > mice_report.log

  1. I got this error message: miRDeep2 started at 18:59:01 mkdir mirdeep_runs/run_28_05_2024_t_18_59_01 Error: Genome file /home/genome/GCA_GRCm39.fa has not allowed whitespaces in its first identifier

then, I removed white spaces in GCA_GRCm39.fa

  1. Rerun the same script and got this message: miRDeep2 started at 7:50:58 mkdir mirdeep_runs/run_30_05_2024_t_07_50_58 The mapped reference id NC_000067.7 from file mice_miRNA_reads_vs_GRCm39_Trim4.arf is not an id of the genome file /home/genome/GCA_GRCm39.fa

Question: Does anyone know why i am getting this message?

Drmirdeep commented 2 months ago

Apparently you have problems with your ids. what is the output of

grep NC_000067.7 mice_miRNA_reads_vs_GRCm39_Trim4.arf |head -n1

and

grep NC_000067.7 /home/genome/GCA_GRCm39.fa

genesio-Ka commented 2 months ago

This is an example of the "fa" file:

062_0_x53637 GGAATGTAAAGAAGTATGTAT 062_53637_x34845 GAGATGAAGCACTGTAGCTCT 062_88482_x23420 GAGGTAGTAGATTGTATAGTT 062_111902_x22650 TGGTCCCCTTCAACCAGCTGT 062_134552_x20278 GGGATGTAGCTCAGTGGTAGA 062_154830_x18293 GAGGTAGTAGGTTGTATAGTT 062_173123_x18191 GAGGTAGTAGGTTGTATGGTT 062_191314_x18030 TTGGTCCCCTTCAACCAGCTGT 062_209344_x16336 GAGGTAGTAGTTTGTACAGTT 062_225680_x12858 TAAACCCAGAAGAGAGTACCA 062_238538_x12687 GAGGTAGTAGGTTGCATAG

grep NC_000067.7 mice_miRNA_reads_vs_GRCm39_Trim4.arf |head -n1 ouput

062_111902_x22650 19 1 19 tggtccccttcaaccagct NC_000067.7 19 20753060 20753078 tggtccccttcaaccagct + 0 mmmmmmmmmmmmmmmmmmm

From: Sebastian Mackowiak @.> Sent: Wednesday, July 3, 2024 5:52 AM To: rajewsky-lab/mirdeep2 @.> Cc: Genesio Mugambi Karere @.>; Author @.> Subject: [EXTERNAL] Re: [rajewsky-lab/mirdeep2] The mapped reference id NC_000067.7 from file mice_miRNA_reads_vs_GRCm39_Trim4.arf is not an id of the genome file /home/genome/GCA_GRCm39.fa (Issue #121)

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Apparently you have problems with your ids. what is the output of

grep NC_000067.7 mice_miRNA_reads_vs_GRCm39_Trim4.arf |head -n1

and

grep mice_miRNA_reads_vs_GRCm39_Trim4.arf /home/genome/GCA_GRCm39.fa

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