Looking at Apul miRNA

in IGV
R
datasets
cod
Author
Affiliation

Steven Roberts

Professor, UW - School of Aquatic and Fishery Sciences

Published

May 16, 2024

16-miRNA vis

Steven Roberts 16 May, 2024

Apul

1 Genome

https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/data/GCF_013753865.1_Amil_v2.1_genomic.fna

Get stuff from NCBI

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_013753865.1/

/home/shared/datasets download genome accession GCF_013753865.1 --include gff3,gtf,gbff

unzip ../data/ncbi_dataset.zip

2 short stack

/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out

See: https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/

head ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/alignment_details.tsv <==
readfile    mapping_type    read_length count
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   <21 120657
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   21  43442
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   22  106124
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   23  65290
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   24  84916
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam U   >24 3225093
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam P   <21 197276
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam P   21  60763
/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged.bam P   22  73569

==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Counts.txt <==
Coords  Name    MIRNA   sRNA-ACR-140-S1-TP2-fastp-adapters-polyG-31bp-merged    sRNA-ACR-145-S1-TP2-fastp-adapters-polyG-31bp-merged    sRNA-ACR-150-S1-TP2-fastp-adapters-polyG-31bp-merged    sRNA-ACR-173-S1-TP2-fastp-adapters-polyG-31bp-merged    sRNA-ACR-178-S1-TP2-fastp-adapters-polyG-31bp-merged
NC_058066.1:152483-152910   Cluster_1   N   2   131 2   1   4
NC_058066.1:161064-161674   Cluster_2   N   57  48  219 32  193
NC_058066.1:172073-172496   Cluster_3   N   36  31  0   36  2
NC_058066.1:203242-203651   Cluster_4   N   14  28  3   17  38
NC_058066.1:204535-205150   Cluster_5   N   3   234 17  13  46
NC_058066.1:205745-206966   Cluster_6   N   914 432 78  247 259
NC_058066.1:210841-211344   Cluster_7   N   315 200 78  2   652
NC_058066.1:349655-351297   Cluster_8   N   497 1236    757 767 22
NC_058066.1:351491-353439   Cluster_9   N   3181    1995    1498    2030    185

==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3 <==
NC_058066.1 ShortStack  sRNA    172680  172697  0   +   .   ID=cgr-miR-1260
NC_058066.1 ShortStack  sRNA    924864  924883  0   -   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130443 2130462 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130445 2130464 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130447 2130466 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130449 2130468 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130451 2130470 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2130453 2130472 0   +   .   ID=mmu-miR-466i-5p
NC_058066.1 ShortStack  sRNA    2424062 2424080 0   +   .   ID=gma-miR1533
NC_058066.1 ShortStack  sRNA    2582838 2582857 0   +   .   ID=mmu-miR-466i-5p

==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/mir.fasta <==
>Cluster_316::NC_058066.1:12757124-12757218(-)
ATGCTTTACTCCTTTGGGAGGGAGGTTAGTGCAGAGGTCATCGTTATTGATGATCTCTGCAATAGCCTGCCTCCCAAAGGAGTTCTACTAGTCC
>Cluster_316.mature::NC_058066.1:12757146-12757168(-)
TGATCTCTGCAATAGCCTGCCT
>Cluster_316.star::NC_058066.1:12757176-12757198(-)
GGAGGTTAGTGCAGAGGTCATC
>Cluster_514::NC_058066.1:20088629-20088720(+)
TTGAATTGTCTGTGGCCTTCACGGCACCCCTTGCTGGAGTTATTTAATAACGCTAGGAAGGGATGCCGGGAAGGAGATGGTACAATGCAAA
>Cluster_514.mature::NC_058066.1:20088678-20088700(+)
ACGCTAGGAAGGGATGCCGGGA

==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3 <==
NC_058066.1 ShortStack  Unknown_sRNA_locus  152483  152910  140 -   .   ID=Cluster_1;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  161064  161674  549 .   .   ID=Cluster_2;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  172073  172496  105 -   .   ID=Cluster_3;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  203242  203651  100 .   .   ID=Cluster_4;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  204535  205150  313 .   .   ID=Cluster_5;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  205745  206966  1930    .   .   ID=Cluster_6;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  210841  211344  1247    .   .   ID=Cluster_7;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  349655  351297  3279    +   .   ID=Cluster_8;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  351491  353439  8889    .   .   ID=Cluster_9;DicerCall=N;MIRNA=N
NC_058066.1 ShortStack  Unknown_sRNA_locus  598651  599068  114 +   .   ID=Cluster_10;DicerCall=N;MIRNA=N

==> ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.txt <==
Locus   Name    Chrom   Start   End Length  Reads   DistinctSequences   FracTop Strand  MajorRNA    MajorRNAReads   Short   Long    21  22  23  24  DicerCall   MIRNA   known_miRNAs
NC_058066.1:152483-152910   Cluster_1   NC_058066.1 152483  152910  428 140 32  0.05    -   UAAGUACUUUAUCAACUAACUCUAGGCA    75  1   130 0   2   0   7   N   N   NA
NC_058066.1:161064-161674   Cluster_2   NC_058066.1 161064  161674  611 549 247 0.2987249544626594  .   UUUUAGCCUAGUGCGGGUUUCCAGACGU    43  25  479 16  4   4   21  N   N   NA
NC_058066.1:172073-172496   Cluster_3   NC_058066.1 172073  172496  424 105 40  0.12380952380952381 -   GCGAUUAUUAACGGCUGGAACGACAGGCGA  16  1   88  1   1   0   14  N   N   NA
NC_058066.1:203242-203651   Cluster_4   NC_058066.1 203242  203651  410 100 45  0.56    .   UUCUGACUCUAUUAGCAACGAAGACUUU    26  1   96  0   1   0   2   N   N   NA
NC_058066.1:204535-205150   Cluster_5   NC_058066.1 204535  205150  616 313 157 0.7763578274760383  .   UCCCAACACGUCUAGACUGUACAAUUUCU   32  3   304 1   1   2   2   N   N   NA
NC_058066.1:205745-206966   Cluster_6   NC_058066.1 205745  206966  1222    1930    416 0.35544041450777203 .   CAAAAGAGCGGACAAAAUAGUCGACAGAUU  716 3   1882    5   10  7   23  N   N   NA
NC_058066.1:210841-211344   Cluster_7   NC_058066.1 210841  211344  504 1247    333 0.7457898957497995  .   UAAUACUUGUAGUGAAGGUUCAAUCUCGA   95  10  1133    7   7   20  70  N   N   NA
NC_058066.1:349655-351297   Cluster_8   NC_058066.1 349655  351297  1643    3279    1165    0.8127477889600488  +   UCAGCUUGGAAAUGACAGCUUUUGACGU    255 27  3141    10  22  17  62  N   N   NA
NC_058066.1:351491-353439   Cluster_9   NC_058066.1 351491  353439  1949    8889    1615    0.4114073574080324  .   UUUCAAAUCAAAGAUCUUCGCAACGAUGA   780 82  8503    34  34  114 122 N   N   NA
wc -l ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
    151 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/alignment_details.tsv
  18896 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Counts.txt
   1446 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3
    228 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/mir.fasta
  18971 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3
  18896 ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.txt
  58588 total
grep -c ">" ../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/*
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/alignment_details.tsv:25
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Counts.txt:0
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3:0
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/mir.fasta:114
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3:0
../output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.txt:0

3 IGV

igv

IGV session file: https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/code/16.1.ivg_session.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Session genome="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/data/GCF_013753865.1_Amil_v2.1_genomic.fna" hasGeneTrack="false" hasSequenceTrack="true" locus="NC_058068.1:0-19500522" version="8">
    <Resources>
        <Resource path="https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.bed" type="bed"/>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3" type="gff3"/>
        <Resource path="http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.gff" type="gff"/>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/known_miRNAs.gff3" type="gff3"/>
    </Resources>
    <Panel height="792" name="FeaturePanel" width="1752">
        <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="false" visible="true"/>
        <Track attributeKey="GCF_013753865.1_Amil_v2.1_genomic.gff" clazz="org.broad.igv.track.FeatureTrack" displayMode="EXPANDED" fontSize="20" groupByStrand="false" height="100" id="http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.gff" name="GCF_013753865.1_Amil_v2.1_genomic.gff" visible="true"/>
        <Track attributeKey="Results.gff3" clazz="org.broad.igv.track.FeatureTrack" colorScale="ContinuousColorScale;0.0;69.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="20" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/deep-dive/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/ShortStack_out/Results.gff3" name="Results.gff3" visible="true"/>
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    <PanelLayout dividerFractions="0.007471980074719801"/>
    <HiddenAttributes>
        <Attribute name="DATA FILE"/>
        <Attribute name="DATA TYPE"/>
        <Attribute name="NAME"/>
    </HiddenAttributes>
</Session