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Hi there

I'm using BAMscale Version: v0.0.5 .
The "scale" utility is reporting "ERROR: BAM file index (.bai) does not exist". The manual check for index (.bai) however shows it does exist. I'm happy to share the BAM file and it's index (.bai) but I'm not sure what is the best way to do it here.

Hi,

is endseq: strand-specific coverages in this context referring to the strand specificity based on the underlying DNA reference or based on sense/antisense RNA transcription for strand-specific RNA libraries?

Thanks!

Hi there,
I tried running BAMscale scale --operation subtract on two ChIPseq files, it processed them swiftly however the resulting bigwig files are causing trouble with downstream tools such as deeptools' plotProfile.
It also appears as bars in the IGV browser rather than the usual signal track as shown:

Converting to wig format using bigWigToWig seems to indicate the bigwigs are fixedStep, could this be the problem?
Any option to output to variableStep bigwig?

Hello,

When I try to do k-means clustering, I receive an error below. As I searched, this is because of NAs present in the data frame. I m not sure how to omit NAs from peakds data. Thanks in advance for your help.

peakds = PrepareDataForPlotting(peakds)
Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
Called from: do_one(nmeth)

--Hi,

i want to emphasize the best peaks and i think to do that i need to compute some statistics using the tpm output.
But i'm not very familiar with stats and i don't known how to do. Do you have some clues or tuto ? Thank you .

best,
L.

Let's say you want to use BAMscale to calculate a library size scaling factor using a command such as the following (example command, not real data)

$ BAMscale scale --operation rna --threads 20 \
--bam 162260/162260.bam \
--bam 162261/162261.bam > BAMscale.log 2>&1

$ grep -P -A 2 "Sample: \d+.bam" BAMscale.log|paste - - - -

Sample: 162260.bam	Total no. of reads: 537060		Library size scale: 0.00	--
Sample: 162261.bam	Total no. of reads: 1883		Library size scale: 1.00	--

If there is huge difference in the number of reads between the largest and smallest library, the estimated Library size scale will be 0.00 due to rounding to only 2 decimal places. Is there some way to either expose an option to make this value user adjustable or just simply set it to maybe 8 decimal places?

Is there a static executable available for MAC OS? It would be a great help.