ibseq

Hi Patrick, They are not trimmed. I got this from the sequencing facility Is there a way to override this? BW Ib > On 29 Apr 2020, at 08:36, Patrick...

zcat IGF112169/FB_S3_L003_R1_001.fastq.gz | grep -P "^[ATGCN]{1,}$" | head -100 | awk '{ print length }' | sort | uniq 149 150 zcat IGF112169/FB_S3_L003_R2_001.fastq.gz | grep -P "^[ATGCN]{1,}$" | head -100...

Can this be overridden? I only have access to these fastqs > On 29 Apr 2020, at 11:02, Patrick Roelli wrote: > > > Those are definitely trimmed. The numbers...

That would be great for all of us! Thanks > On 29 Apr 2020, at 11:06, Patrick Roelli wrote: > > > Right now, no. I can fix it up...

same error after I've updated cite-seq count to v1.4.3 (I had 1.4.2 earlier): [ERROR] Sequence length in R1.fastq.gz is not consistent. Please, trim all sequences at the same length. Exiting...

nothing...it still asking me to trim R1 reads to same length. I have trimmed my R1 to same lenght (149bp and another trim to 140bp), both not working giving me...

I had the right version, but I did as you said, uninstall and install again: [ERROR] Sequence length in R1_001.fastq.gz is not consistent. Please, trim all sequences at the same...

it did run for a while but stopped with this: Traceback (most recent call last): File "/home/ibseq/anaconda3/envs/cite/bin/CITE-seq-Count", line 10, in sys.exit(main()) File "/home/ibseq/anaconda3/envs/cite/lib/python3.7/site-packages/cite_seq_count/__main__.py", line 409, in main ) = processing.merge_results(parallel_results=parallel_results[0])...

the error log file is the one i sent you earlier. I've used 32 cpus do i need more?

the output log file is: Counting number of reads [WARNING] Read1 length is 149bp but you are using 26bp for Cell and UMI barcodes combined. This might lead to wrong...