If -iso-score-threshold value is given, no Clustering.

Question

If -iso-score-threshold value is given, no Clustering.

jkbenotmane opened this issue 3 years ago · 2 comments

Hi, thanks in advance for helping !
I want to find the best setting for the clustering of only minor differing reads (Lymphocyte Receptor Arrangements).
Therefore i tried multiple settings of rattle cluster -iso-score-threshold but it seems like, that any value given to this option leads to no clusters found, even when giving explicitly the default value.
E.g.

${RATTLE_PATH}/rattle cluster \
>         -i 'IGB_CLUSTERS/TRB' \
>         -t ${THREADS} \
>         -o "${OUTDIR}"/CORRECTION/RATTLE_CLUSTERS \
>         --fastq 
RNA mode: 0
Reading fasta file... Done
[================================================================================] 636/636 (100%)28%)
[================================================================================] 292/292 (100%)75%)
Iteration 0.35 complete
[================================================================================] 278/278 (100%)03%)
Iteration 0.3 complete
[================================================================================] 269/269 (100%)83%)
Iteration 0.25 complete
[================================================================================] 264/264 (100%)12%)
Iteration 0.2 complete
[================================================================================] 254/254 (100%)63%)
Iteration 0 complete
Gene clustering done
213 gene clusters found

When giving explicitly the default value 0.3:

${RATTLE_PATH}/rattle cluster \
>         -i 'IGB_CLUSTERS/TRB' \
>         -t ${THREADS} \
>         -o "${OUTDIR}"/CORRECTION/RATTLE_CLUSTERS \
>         --fastq \
>         -iso-score-threshold 0.3
RNA mode: 0
Reading fasta file... Done
Iteration 0.35 complete
Iteration 0.3 complete
Iteration 0.25 complete
Iteration 0.2 complete
Iteration 0 complete
Gene clustering done
0 gene clusters found

What am I doing wrong ?

Answer 1 · 2022-01-27T10:28:32.000Z

Hi Jasim, thanks for your message. Please try adding the *--iso* option, which is to separate reads in gene-like clusters into transcript-like clusters, as the *--iso-**-score-threshold* option is relevant only for that operation. It might be that we must make explicit this dependency of the parameters. If it does not work, please send us some sample data and we can give it a test best Eduardo

…

On Thu, 27 Jan 2022 at 21:13, Jasim K.B. ***@***.***> wrote: Hi, thanks in advance for helping ! I want to find the best setting for the clustering of only minor differing reads (Lymphocyte Receptor Arrangements). Therefore i tried multiple settings of *rattle cluster -iso-score-threshold* but it seems like, that any value given to this option leads to no clusters found, even when giving explicitly the default value. E.g. ${RATTLE_PATH}/rattle cluster \ > -i '/media/milolab/JKB_500GB/COMPARRATTLE_OUT/SPTCR13_no_exon_with_vj_clustering_0_85_rattle_clust/IGB_CLUSTERS/TRB_TRBV7-8_TRBJ1-3.fastq' \ > -t ${THREADS} \ > -o "${OUTDIR}"/CORRECTION/RATTLE_CLUSTERS \ > --fastq RNA mode: 0 Reading fasta file... Done [================================================================================] 636/636 (100%)28%) [================================================================================] 292/292 (100%)75%) Iteration 0.35 complete [================================================================================] 278/278 (100%)03%) Iteration 0.3 complete [================================================================================] 269/269 (100%)83%) Iteration 0.25 complete [================================================================================] 264/264 (100%)12%) Iteration 0.2 complete [================================================================================] 254/254 (100%)63%) Iteration 0 complete Gene clustering done 213 gene clusters found When giving explicitly the default value 0.3: ${RATTLE_PATH}/rattle cluster \ > -i '/media/milolab/JKB_500GB/COMPARRATTLE_OUT/SPTCR13_no_exon_with_vj_clustering_0_85_rattle_clust/IGB_CLUSTERS/TRB_TRBV7-8_TRBJ1-3.fastq' \ > -t ${THREADS} \ > -o "${OUTDIR}"/CORRECTION/RATTLE_CLUSTERS \ > --fastq \ > -iso-score-threshold 0.3 RNA mode: 0 Reading fasta file... Done Iteration 0.35 complete Iteration 0.3 complete Iteration 0.25 complete Iteration 0.2 complete Iteration 0 complete Gene clustering done 0 gene clusters found What am I doing wrong ? — Reply to this email directly, view it on GitHub <#32>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB2LAWWDXEIZNEE4HYDUYELFJANCNFSM5M5ONZIA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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Answer 2 · 2022-01-27T10:49:12.000Z

Hi Eduardo,

thank you for the quick response!
I actually did add --iso in another trial, but the issue was even easier.
I did miss the second "-" for long command-line option
Changing

-iso-score-threshold 0.3

to

--iso-score-threshold 0.3

Solved it.
Thank you and all the best!