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Simon-Leonard / APERO

small RNA detection from paired-end RNA-seq data
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"SAM/BAM header missing or empty" error #4

Open dplazas opened 4 years ago

dplazas commented 4 years ago

Hi, I wanted to use your tool but after installing everything I found the before mentioned error (I am quite new in R). Also, I would like to know whether is possible to use other formats than ".ptt" as input. Finally, I found this Galaxy web: http://bf2i-galaxy.insa-lyon.fr:8080/ but have no idea how to load my data. I hope you can please help me out. Thank you very much in advance. Best

Simon-Leonard commented 4 years ago

Hi, Did you try ton run APERO with the example bam file ? Concerning the ptt file, you can also use a ptt-like tabular file with the same column names than classic ptt format. Bests Simon

dplazas commented 4 years ago

Hi Simon, thank you very much for reply. I am sorry my late reply. No, I didnt try any example, I will and let you know. I am also gonna check the columns structure. Best, Daniel

El vie., 15 may. 2020 a las 5:51, Simon-Leonard (notifications@github.com) escribió:

Hi, Did you try ton run APERO with the example bam file ? Concerning the ptt file, you can also use a ptt-like tabular file with the same column names than classic ptt format. Bests Simon

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dplazas commented 4 years ago

Hi Simon, now I did run the example and got : Error in data.frame(colsplit(ref$Location, "\\..", c("Left", "Right")), : arguments imply differing number of rows: 0, 281 then for 3' Error in APERO_end_detection(work_dir = "/Users/danplaza/", start_table = res, : object 'res' not found what did happen? thank you Daniel

Simon-Leonard commented 4 years ago

Hi Daniel,

Can you check that the annotation file is correctly imported ? After : ptt=read.csv("E:/APERO/NC_016810.ptt",sep="\t",skip=2,header=T,stringsAsFactors = F)

What do you get with head(ptt) ?

Simon

dplazas commented 4 years ago

Hi Simon, thanks for your help. I checked the example ptt file (by head) and showed information related to the website (I guess) <``` <!DOCTYPE html>

... ```> ... hence since the file did not contain the info it should, I copied and pasted the info directly to a new txt file. Once running was done, no text file was created. I also tested only the example bam file, and again, no new text file was found. Finally, I tested my bam files (triplicate) and got " ``` " ``` this is my bam file: [https://www.ebi.ac.uk/ena/data/view/ERR322349] any comments? where the results text should be created? thank you
dplazas commented 4 years ago

(this page does not allow to post the first message!) something like: !DOCTYPE html.... ....html lang="en"... ...head... ....meta charset="utf-8".... .....link rel="dns-prefetch" href="https://github.githubassets.com....