Input file

Input: Table

• Sample name
• Flag for single-end/paired-end
• Location of fastq files in format
  • mate1: location
  • mate2: location
• Fragment
  • mean: value
  • standard deviation: value
• Adaptors
  • 5p: sequence
  • 3p: sequence
• Flag for reverse-complementing sequences

changed title from Input to Input file

changed the description

changed milestone to %Preprocessing

assigned to @boersch

This is the updated template for storing metadata for NGS data: https://labkey.scicore.unibas.ch/labkey/Zavolan%20Group/Test_aboersch/list-grid.view?listId=9

These are column names of fields relevant for further processing (see detailed description of each column in LabKey):

• Path_Fastq_Files
• Sample_Name
• Replicate_Name
• Single_Paired
• Mate1_File
• Mate2_File
• Mate1_Direction
• Mate2_Direction
• Mate1_Adapter
• Mate2_Adapter
• Fragment_Length_Mean
• Fragment_Length_SD
• Quality_Control_Flag

Thanks @boersch. I think we might also need for each mate a 5' and a 3' adapter. So I recommend changing Mate1_Adapter and Mate2_Adapter to:

• Mate1_5p_Adapter
• Mate1_3p_Adapter
• Mate2_5p_Adapter
• Mate2_3p_Adapter

Thanks for the feedback @gypas. I also asked for the feedback Maria and Mihaela. Then I will implement all comments at once.

We also need organism and read length if available (not fragment length).

added Doing label

Actually, these fields are already in the table. The field for the read length is called "Cycles". There are two fields for the organism:

• "Organism" containing the Latin name of the organism, e.g. Mus musculus
• "TaxonID" containing the unique taxon ID, e.g. 10090 for the house mouse

So is there any metadata table available? Maybe the one of Shreemoyee? Even if it is only paired-end or single-end it is ok. I just need it to start testing.

OK, I will prepare it now. I will let you know.

Here is a test input file: https://labkey.scicore.unibas.ch/labkey/Zavolan%20Group/Test_aboersch/list-grid.view?listId=9

Features needed by Snakemake:

samples_tables.tsv features

name	details
fq1	fastq file path mate1
fq2	fastq file path mate2
fq1_3p	3 end adapter in mate1
fq1_5p	5 end adapter in mate1
fq2_3p	3 end adapter in mate2
fq2_5p	5 end adapter in mate2
fq1_polya	(A or G or T or C or N stretches)
fq2_polya	(A or G or T or C or N stretches)
organism	(?)
index_size	(--sjdbOverhang option of STAR index)
multimappers	Number of allowed multimappers in STAR
soft_clip	(--alignEndsType argument of STAR)
pass_mode	(allowed values from STAR --twopassMode )
gtf_filtered	(gtf filtered for nc RNAs)
libtype	(keyword in salmon for mode --libtype argument)
kallisto_directionality	(fr or rf)
mean	(number, provided by experiment)
sd	(number, , provided by experiment)
genome	(fasta file)
gtf	(gtf file)
tr_fasta_filtered	(transcriptome fasta)
kmer	(suggested value 31)
seqmode	(single_end or paired_end)

config values

feature	details
star_indexes	path to the index of STAR
kallisto_indexes	path to the kallisto needed indexes
local_log
output_dir

@katsanto Please take a look on issue #36

The path is: /scicore/home/zavolan/GROUP/resources/homo_sapiens/ENSEMBL_99/

mentioned in merge request !7 (merged)

@katsanto Changed to: /scicore/home/zavolan/GROUP/resources/ENSEMBL_99/homo_sapiens

changed title from Input file to LabKey input file

mentioned in issue #39 (closed)