Issues about using salmon quant on multiple bam files

[ShaowenJ]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? salmon Describe the bug I was trying to do salmon quant on multiple bam files together but got the error.

To Reproduce Steps and data to reproduce the behavior: salmon quant -t /Reference/GRCm39_Gencode/GRCm39.fa --libType A --ont -a ./bamfiles/*.bam -o ./salmon_bulk Specifically, please provide at least the following information:

• Which version of salmon was used?

• How was salmon installed (compiled, downloaded executable, through bioconda)?

• Which reference (e.g. transcriptome) was used?

• Which read files were used?

• Which which program options were used?

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots or terminal output to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. Ubuntu Linux, OSX]
• Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]

Additional context Add any other context about the problem here.

[alexdhill]

Can you head any of the bam files? The fact that they are all *.txt.bam seems suspiciously like they are renamed text files.

Does this happen if you run a single bam file at once?

Would also be helpful to fill out the rest of the missing info requested (To Reproduce, Expected Behavior, Desktop, etc.)

[ShaowenJ]

It doesn’t have a problem with a single bam file. Which is the reason make me wonder maybe my command is wrong. Sure, I can share some of the bam files later today

On Thu, Mar 21, 2024 at 4:48 PM Alex D Hill @.***> wrote:

Can you head any of the bam files? The fact that they are all *.txt.bam seems suspiciously like they are renamed text files.

Does this happen if you run a single bam file at once?

Would also be helpful to fill out the rest of the missing info requested (To Reproduce, Expected Behavior, Desktop, etc.)

— Reply to this email directly, view it on GitHub https://github.com/COMBINE-lab/salmon/issues/920#issuecomment-2013705067, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHJBWLH4NQP66UEUFSFESXDYZNBRHAVCNFSM6AAAAABFBYUNKOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJTG4YDKMBWG4 . You are receiving this because you authored the thread.Message ID: @.***>

[ShaowenJ]

Here is a snapshot from the head of a bam file; the reason why they all have the .txt is that I didn't remove the suffix to name them in the new bam output.

[ShaowenJ]

Actually, I was wondering if I could use this method to help me quantify my Nanopore library with barcode sequence? I have already demultiplexed the ONT library to each individual barcode by using some other tools and generated a meta table with matched barcode and readID. It would be great if you guys have any ideas on how can I generate a barcode-gene count matrix from it. My current workflow is aligning via minimap2 and subset the bam file to each barcode by matching the readID, and use Salmon or other tools to quantify the counts, and compile the matrix together. But it took a very long time and memory. Maybe there's another more efficient way.