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no spikeIn chromosomes found with extention _spikein #924
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just to add that the bam file header is: bam header```bash@hd VN:1.5 SO:coordinate
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Hi Sunta3iouxos, your workflow in general looks good, i.e. createIndices -> DNA-mapping -> ChIPseq. What does Best wishes, Katarzyna |
0 grep -c Chromosome CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spik
es/genome_fasta/genome.fa
1 |
What does the chromosome name in the bacterial fasta look like? Are there any spaces in it? This typically causes issues. |
grep ">" CUT-RUNTools-2.0/assemblies/EB1/Sequence/WholeGenomeFasta/
genome.fa
>Chromosome grep -c " " CUT-RUNTools-2.0/assemblies/EB1/Sequence/WholeGenomeFas
ta/genome.fa
0 |
I added the --spikeinExt Chromosome and it does not complain. Is this correct then? P.S. There are some other warnings, and messages that require new tickets. |
You mean you passed this to With
The chromosome name in the E.coli fasta was renamed from If you'd like to troubleshoot what happens with the chromosome names in the Best wishes, Katarzyna |
Yes, using the
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If you follow a bit the provided information, the _spikein identifier is there but only in the "/spikein_genes.gtf " but nowhere else (at least not in the readable files (so excluding the binary index bowtie2 files. The genome.fa of the bacteria is as follows:
I do not see any specific error. grep ">" CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/genome_fasta/genome.fa
>chr1 1
>chr2 2
>chr3 3
>chr4 4
>chr5 5
>chr6 6
>chr7 7
>chr8 8
>chr9 9
>chr10 10
>chr11 11
>chr12 12
>chr13 13
>chr14 14
>chr15 15
>chr16 16
>chr17 17
>chr18 18
>chr19 19
>chrX X
>chrY Y
>chrM MT
>GL456210.1 GL456210.1
>GL456211.1 GL456211.1
>GL456212.1 GL456212.1
>GL456213.1 GL456213.1
>GL456216.1 GL456216.1
>GL456219.1 GL456219.1
>GL456221.1 GL456221.1
>GL456233.1 GL456233.1
>GL456239.1 GL456239.1
>GL456350.1 GL456350.1
>GL456354.1 GL456354.1
>GL456359.1 GL456359.1
>GL456360.1 GL456360.1
>GL456366.1 GL456366.1
>GL456367.1 GL456367.1
>GL456368.1 GL456368.1
>GL456370.1 GL456370.1
>GL456372.1 GL456372.1
>GL456378.1 GL456378.1
>GL456379.1 GL456379.1
>GL456381.1 GL456381.1
>GL456382.1 GL456382.1
>GL456383.1 GL456383.1
>GL456385.1 GL456385.1
>GL456387.1 GL456387.1
>GL456389.1 GL456389.1
>GL456390.1 GL456390.1
>GL456392.1 GL456392.1
>GL456393.1 GL456393.1
>GL456394.1 GL456394.1
>GL456396.1 GL456396.1
>JH584292.1 JH584292.1
>JH584293.1 JH584293.1
>JH584294.1 JH584294.1
>JH584295.1 JH584295.1
>JH584296.1 JH584296.1
>JH584297.1 JH584297.1
>JH584298.1 JH584298.1
>JH584299.1 JH584299.1
>JH584300.1 JH584300.1
>JH584301.1 JH584301.1
>JH584302.1 JH584302.1
>JH584303.1 JH584303.1
>JH584304.1 JH584304.1
>Chromosome
in the genome.fa.fai the correct size is reported: grep Chromosome CUT-RUNTools-2.0/assemblies/mm10_gencodeM1
9_spikes/genome_fasta/genome.fa.fai
Chromosome 4686137 2776387558 60 61
INTERESTINGLY grep Chromosome /home/tgeorgom/CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes/annotation/spikein_genes.gtf | head -n 1
**Chromosome_spikein** ena CDS 190 252 . + 0 exon_number "1"; gene_biotype "protein_coding"; gene_id "ECDH10B_0001"; gene_name "thrL"; gene_source "ena"; gene_version "1"; p_id "P2524"; protein_id "ACB01206"; protein_version "1"; transcript_biotype "protein_coding"; transcript_id "ACB01206"; transcript_name "thrL-1"; transcript_source "ena"; transcript_version "1"; tss_id "TSS3237";
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I can check if I can reproduce this issue here. |
Hi there, |
Hi, could you send me the link to this bacterial genome fasta? Best wishes, Katarzyna |
Hi Katarzyna and everyone else,
I can not run the spikeIns strings for Chip-seq, this is a CUT&RUN protocol that has the bacteria cary over that can be used to "normalize the samples".
this is the full error:
The steps I have followed:
createIndices -o CUT-RUNTools-2.0/assemblies/mm10_gencodeM19_spikes --tools bowtie2 -j 6 --local --genomeURL CUT-RUNTools-2.0/assemblies/GRCm38_gencode_release19/genome_fasta/genome.fa --gtfURL CUT-RUNTools-2.0/assemblies/GRCm38_gencode_release19/annotation/genes.gtf --spikeinGenomeURL CUT-RUNTools-2.0/assemblies/EB1/Sequence/WholeGenomeFasta/genome.fa --spikeinGtfURL CUT-RUNTools-2.0/assemblies/EB1/Annotation/Genes/genes.gtf --blacklist CUT-RUNTools-2.0/blacklist/mm10.blacklist_merged.bed mm10_gencodeM19_spikes DNA-mapping -i /mnt/c/AP01/ -o /mnt/c/AP01/bamSpikes --local --trim --trimmer fastp --trimmerOptions "--trim_poly_g --trim_poly_x -Q -L --correction" --dedup --mapq 2 -j 8 mm10_gencodeM19_spikes ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --peakCaller Genrich --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spike /mnt/c/AP01/bamSpikes/H3K36me3_chip_type.yaml
and this is my hybrid genome yalm
mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/shared/organisms/mm10_gencodeM19_spikes.yaml
indexed genome:
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