pongorlorinc

Hi Maco, I see you have a single-end BAM file, but using paired-end mode for quantification. Could you try removing the "-p" flag? It should work then. Best wishes Lorinc...

Hmmm, it means that there is a mismatch of chromosomes between the gtf and bam file. Did you use the same gtf during alignment? On Mon, May 30, 2022, 9:19...

What error do you get with this other bam file? On Tue, May 31, 2022, 4:52 AM marco91sol ***@***.***> wrote: > At the end, it worked even if there was...

Seems like the bam file is not sorted. That may cause an issue. Could you sort the bam file and retry quantification? On Tue, May 31, 2022, 8:07 AM marco91sol...

Glad to hear it! On Tue, May 31, 2022 at 10:42 AM marco91sol ***@***.***> wrote: > At the moment, It's working... There were some issues with the *samtools > sort*...

Hi Zoe-github2! Based on your BAM file in the third figure, it seems that the reads were aligned to the transcriptome, and not to the genome. To my knowledge, TPMcalculator...

Thanks for the update. I see you used the TranscriptomeSAM option which also generates the transcriptome based BAM file. Did you run TPMcalculator with the transcriptome or genome aligned BAM?...

Hi Zoe, A small followup question. Are the missing chromosomes part of the genome fasta file? If you run a grep ">" genome.fasta It should output all fasta entries (where...

Hi, To my understanding the END-seq is sequenced in a strand specific manner, so the strand information can be retrieved by the alignment orientation, which is used by BAMscale. Hope...

Hi, when you specify the stranded options, BAMscale follows the strand of the mapped read, as in the flag that specifies if the read maps to the positive or negative...