Single-end reads

[kathrinannaotte]

Hi Ramon,

I have a bunch of SE reads for creating a de-novo transcriptome. Is this possible with TransPi? So far I tried the full analysis but failed already at the fastp step, as the program is already missing the file with the reverse reads (-I null):

`Error executing process > 'fastp (Pool_348_L13_S13_L002_R1)'

Caused by:
Process fastp (Pool_348_L13_S13_L002_R1) terminated with an error exit status (255)

Command executed:

fastp -i Pool_348_L13_S13_L002_R1.fastq.gz -I null -o left-Pool_348_L13_S13_L002_R1.filter.fq -O right-Pool_348_L13_S13_L002_R1.filter.fq --detect_adapter_for_pe --average_qual 5 --overrepresentation_analysis --html Pool_348_L13_S13_L002_R1.fastp.html --json Pool_348_L13_S13_L002_R1.fastp.json --thread 6 --report_title Pool_348_L13_S13_L002_R1

v=$( fastp --version 2>&1 | awk '{print $2}' )
echo "fastp: $v" >fastp.version.txt

Command exit status:
255

Command output:
(empty)

Command error:
ERROR: Failed to open file: null
`
Is there anything I can do? My installation works with your test data and other PE data.
In principle, all the programs should work with SE reads as well, right?

Thank you so much!
Kathrin

[rivera10]

Hello @kathrinannaotte,

Unfortunately, TransPi is only for paired-end reads. However, I can create new processes to do the assemblies with single reads and perform some of the steps, similar to the paired-end reads. I'll work something and let you know. How many files do you have?

Best,
Ramón

[kathrinannaotte]

Hi @rivera10,

if you could create a SE version of TransPi, that would be awesome, thank you!

In total, I have 35 files which have around 600M reads altogether. If this takes too long to assemble I might downsample them or create assemblies of subsets from the data, have not decided on this yet.

All the best
Kathrin

[sunnyEV]

Hi,
Any updates on TansPi for SE ?