Hello, I have another question 😅 I'm not sure I understand the content of the smallRNA file for human. I took a look at the source https://github.com/ulelab/smallRNAs/blob/main/Sources.md and I see that the first file (tRNA) is longer than the smallRNA file given with the pipeline and there's almost only tRNA in the file. So I'm wondering, what's really in this file ? How those sequences were choosen please ?

Hello again, Here's my next error in the execution of the pipeline. PureClip seems to have trouble for part of the data. Could it be a memory error or is it to do with the data please ?

[85/89f50f] process > get_software_versions [100%] 1 of 1 ✔️ [b0/f34aa6] process > generate_premap_index (Homo_sapiens.smallRNA.fa.gz) [100%] 1 of 1 ✔️ [d7/47f7cd] process > generate_fai (GRCh38.p13.genome.fa) [100%] 1 of 1 ✔️ [3a/dcce0b] process > generate_star_index (GRCh38.p13.genome.fa) [100%] 1 of 1 ✔️ [79/306e25] process > icount_segment (gencode.v34.annotation.gtf) [100%] 1 of 1 ✔️ [64/e3a3f6] process > fastqc (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [3f/e98335] process > move_umi (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [fa/0cde74] process > cutadapt (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [b2/a60dcb] process > premap (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [dd/843fe1] process > align (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [40/8114ad] process > preseq (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [e9/03c5ee] process > dedup (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [3d/41d84f] process > rseqc (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [48/db8344] process > get_crosslinks (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [6a/f7c583] process > icount_peak_call (PTBP1iCLIP_siCtrl_repl1_s) [ 25%] 1 of 4 [68/f63dbe] process > paraclu_peak_call (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [17/05d893] process > pureclip_peak_call (PTBP1iCLIP_siMATR3_rep2_s) [ 57%] 4 of 7, failed: 4, retries: 3 [d3/d99fb6] process > piranha_peak_call (PTBP1iCLIP_siCtrl_repl1_s) [100%] 4 of 4 ✔️ [- ] process > clipqc [ 0%] 0 of 1 [- ] process > multiqc - [ac/bbfcc0] process > output_documentation [100%] 1 of 1 ✔️ Error executing process > 'pureclip_peak_call (PTBP1iCLIP_siMATR3_rep2_s)' Caused by: Process

pureclip_peak_call (PTBP1iCLIP_siMATR3_rep2_s)

terminated with an error exit status (134) Command executed: pureclip \ -i PTBP1iCLIP_siMATR3_rep2_s.dedup.bam \ -bai PTBP1iCLIP_siMATR3_rep2_s.dedup.bam.bai \ -g GRCh38.p13.genome.fa \ -nt 20 \ -bc 0 -dm 8 -iv 'all' \ -o "PTBP1iCLIP_siMATR3_rep2_s.sigxl.bed" \ -or "PTBP1iCLIP_siMATR3_rep2_s.8nt.peaks.bed" pigz PTBP1iCLIP_siMATR3_rep2_s.sigxl.bed PTBP1iCLIP_siMATR3_rep2_s.8nt.peaks.bed Command exit status: 134 Command output: b0:0 mean:1 k:1 tp:0.00807885 initial transition frequencies: 0: 1 1 1 1 1: 1 1 1 1 2: 1 1 1 1 3: 1 1 1 1 Build HMM ... * Transition probabilitites * 0: 0.25 0.25 0.25 0.25 1: 0.25 0.25 0.25 0.25 2: 0.25 0.25 0.25 0.25 3: 0.25 0.25 0.25 0.25 Baum-Welch ... learn binomial parameter .. 0th iteration computeEmissionProbs() computeStatePosteriorsFB() updateDensityParams() ** Convergence ! ** learn gamma parameter .. 0th iteration computeEmissionProbs() computeStatePosteriorsFB() updateDensityParams() ** Convergence ! ** learn binomial parameter .. 0th iteration computeEmissionProbs() computeStatePosteriorsFB() updateDensityParams() ** Convergence ! ** learn gamma parameter .. 0th iteration computeEmissionProbs() computeStatePosteriorsFB() updateDensityParams() ** Convergence ! ** Apply learned parameters to whole dataset ... chr1 Get preprocessed intervals: Compute KDEs ... Estiamte Ns ... 1 Apply learned HMM: applyParameters Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred ERROR: Can't find contigName in store.contigNameStore!all terminate called after throwing an instance of 'boost:exception detailclone impl&lt;boostexception detailerror info injector&lt;std:domain_error> >' what(): Error in function boost:math:binomial_distribution<long double>:binomial distribution Success fraction argument is -nan, but must be >= 0 and <= 1 ! .command.sh: line 9: 226464 Aborted (core dumped) pureclip -i PTBP1iCLIP_siMATR3_rep2_s.dedup.bam -bai PTBP1iCLIP_siMATR3_rep2_s.dedup.bam.bai -g GRCh38.p13.genome.fa -nt 20 -bc 0 -dm 8 -iv 'all' -o "PTBP1iCLIP_siMATR3_rep2_s.sigxl.bed" -or "PTBP1iCLIP_siMATR3_rep2_s.8nt.peaks.bed"

Hello! I am new to using the nextflow CLIPseq pipeline and it seems it will only run with DSL2 with the current version of nextflow. Is there an easy way to migrate the script to DSL2? Thanks for any advice!

Hello, I received my CLIPseq data. First step is to demultiplex. The software runs just fine (ultraplex) but I have questions. The plateform has trimmed the reads so now it should begin with the UMI (NNNN) then the 8 barcodes caracteres then again NN that just separate the reads and the barcodes (from 5' to 3'). When I give the barcode for demultiplexing with this form NNNNXXXXXXXXNN, the software put 6 N as UMI (the 4 first that are the UMI and the 2N at the end that plays separators). Is that correct ? I would say that it's not a probleme for deduplication but as I've never done that before I'm a bit naive and maybe I don't anticipate a probleme in doing it that way. What do you think please ? Also, I was wondering the number of mismatch to allow for the barcodes. If I set it at 2 is that enougth (barcodes of 8 caracteres and 6 conditions to separate) ? Is it too much ? Do I have to take into account the differences between the barcodes to choose ? What are usually the criteria to decide please ? At last, is there any other parameters that should retain my attention or can I leave it to default ? Like the reads qualité maybe ? I appreciate any help, I'm eager to learn here but Google is my only help and it only goes so far... Best,

Hello everyone, I was wondering if it's possible to launch the clipseq pipeline only until mapping with STAR including but not the next steps ? Also, why the deduplication is done after the mapping, it does not seem logical to me but then again I'm new to this... Thanks for your help 🙂

Coud you please give me an idea of the proportion of reads that typically mapped uniquely or not (but not discarded) after mapping with STAR ?

Hi all, I am looking to start contributing time to bringing clipseq to release. I also plan to contribute a chem-clip subworkflow that includes ADAR mutation analysis and DEL deduplication. I see the feat 2.0 branch on github, but I am hoping to speak to a developer to help orient myself to the status of this project. If anyone is willing to brief me on the latest developments, let me know! 🙂

Hi all, I'm unfortunately unable to make the hackathon next week due to other work commitments (boo) but I'd be happy to arrange amongst ourselves a hackathon day or two in the weeks after - I'll make a poll here for some dates!

Emoji react to the best dates for you!

Friday 7th November

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Week starting Monday 24th November

(@Svetlana L @Melina Klostermann @Alex T @Simran Chhabria @Michael Jones @Karen Irawan)

Okay! So lets go with Monday 10th November - perhaps starting from 11.30am BST? Thats 12.30pm for the europeans, then Simran can join over the course of the afternoon, I can stay online into the evening here to cross over more with Simran

hello 🙂 will start things in 10 minutes here: Charlotte Capitanchik is inviting you to a scheduled Zoom meeting. Topic: Charlotte Capitanchik's Zoom Meeting Time: Nov 10, 2025 11:30 AM London Join Zoom Meeting https://crick.zoom.us/j/69358143417?pwd=j6a7BXyTqdDmbLZNCxebLibCpGdC8w.1 Meeting ID: 693 5814 3417 Passcode: 542702

This would be the bindingSiteFinder flowchart. I added what needs to be done as far as I remember for the modules

We fixed a couple of things and taking a break! Will be back at 2.20pm GMT @Simran Chhabria

hi! Charlotte's said we're going to rejoin a little later at 2:40pm now if that's OK with everyone! see you then

new parclip tools maybe we could incorporate @Svetlana L? https://www.biorxiv.org/content/10.1101/2025.11.17.688892v1

Random question: is there no public database of all processed iCLIP datasets (similar to ENCODE for eCLIP)?

Hi everyone, I've been working for the past few months on updating this pipeline, hoping to submit to nf-core for review in the coming months. I was wondering if there was any interest in forming a group to finalise updates for submission at the hackathon in October?

Hihi, I have maybe a bit of a side question ... I was asked what type of control I would recommend apart from the typical eCLIP SM Input control for a iCLIP experiment. So far we are always using CLIP data without controls and instead have peakcallers that do not need controls ... however, sometimes I feel from a computational point of view, having a control could make life much easier ... I have the feeling that different PIs have very strong opinions on this ^^ but how are you handling this? Any recommendations for a good control? Or would you also say it is better to continue computational analyses without controls?

Hello 🙂 Regarding the hackatron I saw that the nf-core webpage says: The nf-core Hackathon will only be held in-person. Will we still use the same days virtually on our own? Or are you joining in Barcelona? I recruited Felix a new phD student in our group, who would join also 🙌 (He build his own nextflow splicing pipeline so he has some nextflow experience as well)