No Chimeric.out.junction file generated

[jtquach1]

Hi,

I ran STAR using this command:

STAR --runThreadN $NSLOTS --genomeDir $ref_genome_path --readFilesIn ${sim_data_path}sim1_reads_1.fq.renamed.fq ${sim_data_path}sim1_reads_2.fq.renamed.fq

and based on the produced Log.out file from STAR, the default value for chimOutType is Junctions.

I did run STAR Fusion using the output from STAR, and STAR Fusion generated a Chimeric.out.junction file. However, I did not get a Chimeric.out.junction file for STAR.

My apologies if this seems like a "noob"-ish question; I am still quite new to using the software.

[jtquach1]

Ah, I forgot to mention that I compiled STAR by doing make in the source folder, instead of the independent static executables that were already provided. I'm not sure if this would have affected the output, but I did get some error messages from compiling STAR in the source folder.

[brianjohnhaas]

Hi, In case it helps, here's the command that we run in STAR-Fusion: STAR --genomeDir ${star_index_dir} \ --readFilesIn ${left_fq_filename} ${right_fq_filename} \ --twopassMode Basic \ --outReadsUnmapped None \ --chimSegmentMin 12 \ --chimJunctionOverhangMin 12 \ --alignSJDBoverhangMin 10 \ --alignMatesGapMax 100000 \ --alignIntronMax 100000 \ --chimSegmentReadGapMax 3 \ --alignSJstitchMismatchNmax 5 -1 5 5 \ --runThreadN ${THREAD_COUNT} \ --outSAMstrandField intronMotif \ --outSAMunmapped Within \ --outSAMtype BAM Unsorted \ --outSAMattrRGline ID:GRPundef \ --chimMultimapScoreRange 10 \ --chimMultimapNmax 10 \ --chimNonchimScoreDropMin 10 \ --peOverlapNbasesMin 12 \ --peOverlapMMp 0.1 \ --chimOutJunctionFormat 1 # required as of STAR v2.6.1

…

On Tue, Jun 18, 2019 at 4:05 PM Joyce Quach ***@***.***> wrote: Ah, I forgot to mention that I compiled STAR by doing make in the source folder, instead of the independent static executables that were already provided. I'm not sure if this would have affected the output, but I did get some error messages from compiling STAR in the source folder. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#665?email_source=notifications&email_token=ABZRKX3DLNOFUKX2OXUMGWTP3E5ZNA5CNFSM4HZDJGIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODX7ZV3I#issuecomment-503290605>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKXYUUYITYGYUUFDOAN3P3E5ZNANCNFSM4HZDJGIA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[jtquach1]

My apologies once again!

I forgot to mention that the version of STAR I am running is 2.7.0.f (as to work with the current reference genome I'm using) and that STAR Fusion is on version 1.6.0.

[brianjohnhaas]

you need to include this option: --chimOutJunctionFormat 1 in order to get the chim junction out file

…

On Tue, Jun 18, 2019 at 4:39 PM Joyce Quach ***@***.***> wrote: My apologies once again! I forgot to mention that the version of STAR I am running is 2.7.0.f (as to work with the current reference genome I'm using) and that STAR Fusion is on version 1.6.0. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#665?email_source=notifications&email_token=ABZRKX3OLGN6M3KAMT2ZG53P3FBZPA5CNFSM4HZDJGIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODX74U5Q#issuecomment-503302774>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKX6APK2MG5T2LDG7453P3FBZPANCNFSM4HZDJGIA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[jtquach1]

Ah, thank you! I will try that.

[jtquach1]

Hi,

I still did not get the Chimeric.out.junction file as an output for STAR alone; this time, I had used this command

STAR \
        --runThreadN $NSLOTS \
        --genomeDir $ref_genome_path \
        --readFilesIn ${sim_data_path}sim1_reads_1.fq.renamed.fq ${sim_data_path}sim1_reads_2.fq.renamed.fq \
        --outFileNamePrefix /home/joyce.quach001/STAR_Align_Outputs/ \
        --chimOutType Junctions \
        --chimOutJunctionFormat 1

The last three lines are new (I decided to put the outputs in a folder for organizing purposes).

Apologies again for the noob-ness; I'm running STAR separate from STAR Fusion since I'm working with my mentor so they see how STAR Fusion can be improved.

[alexdobin]

Hi Joyce,

if you run STAR standalone (i.e. not STAR-Fusion), you would also need
--chimSegmentMin 12 to get chimeric output. However, I would recommend all parameters from STAR-Fusion that Brian suggested above.

Cheers
Alex

[jtquach1]

Thank you so much, Brian and Alex!

(Pardon me for not adding the question label.)