Closed monikaheinzl closed 7 months ago
Hello Monika,
Can you post the commands you used for generating the png?
I adapted them from issue #153. But here they are:
samtools view -b input.bam chr2L > out.bam
samtools view -b -F796 -@50 out.bam | bedtools bamtobed -i stdin | awk -v OFS="\t" '{if ($6=="-"){print $1,$2,$3,$4,$5,$6} else if ($6=="+") {print $1,$2,$3,$4,$5,$6}}' | bedtools genomecov -bg -5 -i stdin -g $chrom.sizes | bedtools sort -i stdin > tmp2
bedGraphToBigWig tmp2 $chrom.sizes unstranded.bw
python build_pwm_from_bigwig.py -i unstranded.bw -g $genome -o DHS_no_shift -cr "chr2L" -c $chrom.sizes
Hello @monikaheinzl,
DNase I cleavage logo is known to be pretty variable -
I was expecting to see something closer to any of these representations. But the PWM your showing is very different. So can you check for the following (1) if there is some problem with the build or preprocessing resulting in the bam? Cross check your individual bams that were merged, do they result in the same PWM? cross check if this is coming from DNase experiment?
If it is none of this let me know - I can suggest an alternate version of the repo that will bypass this error. But be very sure that none of the above is happening.
(Image source: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-019-1642-2/MediaObjects/13059_2019_1642_MOESM1_ESM.pdf)
Best, Anu
Hi,
Ok, thanks for your help already! I will follow your suggestions and then come back to you.
Best, Monika
Closing this due to inactivity, feel free to open this if you continue to see issues.
Hi,
I have a similar issue as in #153 and #169, while training the bias model for my Drosophila DNase-seq data. I have mapped my raw fastq files with Bowtie and MACS2, and I didn’t do any shifting to the data. There is also no inconsistency between the genomic versions of the BAM and BED files (see a screenshot later). Still, I get the following error:
Here is also my command for training the bias model:
As suggested in issue #153, I have also generated the PWM for my BAM file:![image](https://github.com/kundajelab/chrombpnet/assets/38460332/5c6956c7-a678-4c9d-ab82-9827cb5069a5)
Here is also an example of my peak file:
Many thanks for your help, Monika