bamCaverage output .bw file can't be viewed correct by IGV

[ShaokunPan]

Hi

I use the sorted .bam file as input and .bw file is the output, there was no error reported, when using bamCaverage. The sorted .bam file can be viewed using IGV corrected, but the .bw file can't be viewed and no error reported. Can someone help me? Thanks!

deeptools 3.5.1 python: 3.9.3 IGV: 2.12.0

bamCoverage --bam ./sort/OM8_S8_2019nCoV.mapped.sort.bam
-o OM8_S8_2019nCoV.SeqDepth.bw
--outFileFormat bigwig
-p 20
--binSize 1

log: bamFilesList: ['./sort/OM8_S8_2019nCoV.mapped.sort.bam'] binLength: 1 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 20 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 1 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000

[dpryan79]

Can you post the bigWig somewhere so I can more easily debug this?

[aslisadli]

I am experiencing the same issue. What was the solution for that problem? Thanks.

[dpryan79]

@aslisadli There was never any follow-up from the original poster to debug the cause. Can you make your bigWig available to us to debug this?

[aslisadli]

Thanks a lot for your quick reply. I am very new to bioinformatics analysis, possibly doing something wrong but could not figure it out. I aligned my samples with Bowtie2 to S.cerevisiae genome. Then did SAM to BAM conversion, followed by coordinate sorting of BAM files and indexing. I used sorted BAM files to make bigwig files. Although programme runs fine and I got a bigwig file I can not visualize it with IGV(I can see BAM tracks in IGV). I could not attach bigwig file here and don't know how to make it available to you. Sorry if there is a very simple mistake that I could not see and taking your time.

[dpryan79]

Please upload the file to dropbox or google drive or similar and send a link to [email protected]

[dpryan79]

I downloaded one of the yeast chromosomes from NCBI and the most recent version of IGV. I can't seem to reproduce the error:

[aslisadli]

Thanks a lot. I tried the single chromosome fasta download using the INSDC code GenBank: BK006935.2 and it worked. However when I tried to use the genome already in IGV system it does not work. Finally I figured out that I needed to use indexing my reference using the ".fasta" file not the ".fna". Fna files gives chromosomes different names that does not match with IGV hosted genomes.

Thanks again for your help

On Tue, Apr 11, 2023 at 3:30 PM Devon Ryan @.***> wrote:

I downloaded one of the yeast chromosomes from NCBI and the most recent version of IGV. I can't seem to reproduce the error:

[image: image] https://user-images.githubusercontent.com/6399000/231280979-94d1353b-4ed5-45af-a23c-115b6e2734d4.png

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