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scottzijiezhang / MeRIPtools

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get a NA result #18

Open Jiaxuecao opened 3 years ago

Jiaxuecao commented 3 years ago

Thank you for giving us this fabulous tool. I get a NA result, hopefully you can help me.

radar <- countReads(samplenames = c("E601","E602","E751","E752"), gtf = "/Users/jiaxue/Desktop/hisat_indexed_reference/Capra_hircus.ARS1.104.gtf", bamFolder = "/Users/jiaxue/Desktop/BAM", modification = "m6A", fragmentLength = 50, outputDir = "Users/jiaxue/Desktop/result", threads = 20, binSize = 50) Reading gtf file to obtain gene model Filter out ambiguous model... Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Gene model obtained from gtf file... counting reads for each genes, this step may takes a few hours.... Hyper-thread registered: TRUE Using 20 thread(s) to count reads in continuous bins... Time used to count reads: 298.643309915066 mins... Warning message: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.

summary(radar) MeRIP dataset of 4 samples. Read count quantified in 50-bp consecutive bins on the transcript. The total read count for Input and IP samples are (Million reads): E601 E602 E751 E752 Input NA NA NA NA IP NA NA NA NA

XuJahcenia commented 2 years ago

Hi. Have you solved this problem yet? I got the exactly problem as you did.

mohansri1 commented 2 years ago

@Jiaxuecao @XuJahcenia were you able to solve this issue?

mohansri1 commented 2 years ago

I was able to figure it out- make sure to run the countReads function with "paired = TRUE" if you have paired-end sequencing data. The default is set to single-end sequencing ("paired = FALSE").