STAR alignment for multiple lane fastq

[Pitithat-pu]

Hi Developers,
I ran into a problem regarding STAR alignment using multiple lane fastqs.
Given input readindex file contain as follows
sample1 run1 path_to_file/mRNA_L005_R1_001_val_1.fq.gz fastq FqRd1
sample1 run1 path_to_file/mRNA_L005_R2_001_val_2.fq.gz fastq FqRd2
sample1 run1 path_to_file/mRNA_L006_R1_001_val_1.fq.gz fastq FqRd1
sample1 run1 path_to_file/mRNA_L006_R2_001_val_2.fq.gz fastq FqRd2

Here is the command generated by nf
STAR --runThreadN 1 --genomeDir hs38 --readFilesIn mRNA_L005_R1_001_val_1.fq.gz mRNA_L006_R1_001_val_1.fq.gz mRNA_L005_R2_001_val_2.fq.gz mRNA_L006_R2_001_val_2.fq.gz --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --readFilesCommand pigz -p1 -dc --outSAMtype BAM Unsorted --outStd BAM_Unsorted --quantMode TranscriptomeSAM --outSAMattrRGline ID:run140212_SN758_0152_BC3ETGACXX PU:run140212_SN758_0152_BC3ETGACXX SM:41_Hf02_LiHe_Ct_replicate1 | samtools sort -@ 0.5 -m 536870912 - run140212_SN758_0152_BC3ETGACXX_m4_n10_toGenome

I found that the mapping process is not actually running even though the workflow tell nothing wrong. Actually the workflow didn't run anything.

I am asking whether it's possible to change how to supply mapping process for STAR through --readFilesIn by same way shown here. With comma separates different lanes.

Looking forward to your response

[emi80]

Hi, apologies for the late reply. I see the issue and I think we can add the support to run STAR with multiple lanes fastqs as you suggest. You should get noticed as soon as I implement it and close the issue. By the way, the pipeline did not give any error because I think the command line was fine for STAR and it could run (in a wrong way) without errors. Best, Emilio

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On Tue, May 29, 2018 at 12:15 AM, Pitithat Puranachot < ***@***.***> wrote: Hi Developers, I ran into a problem regarding STAR alignment using multiple lane fastqs. Given input readindex file contain as follows sample1 run1 path_to_file/mRNA_L005_R1_001_val_1.fq.gz fastq FqRd1 sample1 run1 path_to_file/mRNA_L005_R2_001_val_2.fq.gz fastq FqRd2 sample1 run1 path_to_file/mRNA_L006_R1_001_val_1.fq.gz fastq FqRd1 sample1 run1 path_to_file/mRNA_L006_R2_001_val_2.fq.gz fastq FqRd2 Here is the command generated by nf STAR --runThreadN 1 --genomeDir hs38 --readFilesIn mRNA_L005_R1_001_val_1.fq.gz mRNA_L006_R1_001_val_1.fq.gz mRNA_L005_R2_001_val_2.fq.gz mRNA_L006_R2_001_val_2.fq.gz --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --readFilesCommand pigz -p1 -dc --outSAMtype BAM Unsorted --outStd BAM_Unsorted --quantMode TranscriptomeSAM --outSAMattrRGline ID:run140212_SN758_0152_BC3ETGACXX PU:run140212_SN758_0152_BC3ETGACXX SM:41_Hf02_LiHe_Ct_replicate1 | samtools sort -@ 0.5 -m 536870912 - run140212_SN758_0152_ BC3ETGACXX_m4_n10_toGenome I found that the mapping process is not actually running even though the workflow tell nothing wrong. Actually the workflow didn't run anything. I am asking whether it's possible to change how to supply mapping process for STAR through --readFilesIn by same way shown here <https://groups.google.com/forum/#!msg/rna-star/mqMzbWpKRA0/iW-S8c8bm5EJ> Looking forward to your response — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#31>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACof_NUzFywppGQ3FReFobgwc9JV4AmNks5t3HcNgaJpZM4UQo8W> .