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Hi <@U03SLE7RBAS>, once more. I have finished a ru...
# riboseq
f
Hi @Jonathan Manning, once more. I have finished a run today, and suspect that domething funky is going on with the result files. I synced down the entire folder 
/alignments/star/deduplicated
, which contains 12 
.bam
and 
.bam.bai
files (4 x 3 replicates). Despite their inconspicious names, I suspect that they somehow are a mix of genome and transcriptome alignments! I had a look at the number of lines in the BAM header:
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for i in *bam; do samtools view -H $i | wc -l; done                                                                      24
    7132
    7132
      24
    7132
      24
      24
      24
      24
    7132
      24
      24
This looks like hearty mix of 8 genomic (yeast), and 4 transcriptome BAMs, is this possible at all?
This is one sort:
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@HD	VN:1.4	SO:coordinate
@SQ	SN:I	LN:230218
@SQ	SN:II	LN:813184
@SQ	SN:III	LN:316620
@SQ	SN:IV	LN:1531933
@SQ	SN:V	LN:576874
@SQ	SN:VI	LN:270161
@SQ	SN:VII	LN:1090940
@SQ	SN:VIII	LN:562643
@SQ	SN:IX	LN:439888
@SQ	SN:X	LN:745751
@SQ	SN:XI	LN:666816
@SQ	SN:XII	LN:1078177
@SQ	SN:XIII	LN:924431
@SQ	SN:XIV	LN:784333
@SQ	SN:XV	LN:1091291
@SQ	SN:XVI	LN:948066
@SQ	SN:Mito	LN:85779
@PG	ID:STAR	PN:STAR	VN:2.7.11b	CL:/opt/conda/bin/STAR-avx2   --runThreadN 12
And this is the other:
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@HD	VN:1.6	SO:coordinate
@SQ	SN:YAL069W_mRNA	LN:315
@SQ	SN:YAL068W-A_mRNA	LN:255
@SQ	SN:YAL068C_mRNA	LN:363
@SQ	SN:YAL067W-A_mRNA	LN:228
@SQ	SN:YAL067C_mRNA	LN:1782
@SQ	SN:YAL066W_mRNA	LN:309
@SQ	SN:YAL065C_mRNA	LN:387
@SQ	SN:YAL064W-B_mRNA	LN:381
@SQ	SN:YAL064C-A_mRNA	LN:381
@SQ	SN:YAL064W_mRNA	LN:285
@SQ	SN:YAL063C-A_mRNA	LN:291
@SQ	SN:YAL063C_mRNA	LN:3969
@SQ	SN:YAL062W_mRNA	LN:1374
@SQ	SN:YAL061W_mRNA	LN:1254
@SQ	SN:YAL060W_mRNA	LN:1149
@SQ	SN:YAL059C-A_mRNA	LN:423
@SQ	SN:YAL059W_mRNA	LN:639
@SQ	SN:YAL058W_mRNA	LN:1509
@SQ	SN:YAL056C-A_mRNA	LN:351
@SQ	SN:YAL056W_mRNA	LN:2643
@SQ	SN:YAL055W_mRNA	LN:543
@SQ	SN:YAL054C_mRNA	LN:2142
@SQ	SN:YAL053W_mRNA	LN:2352
@SQ	SN:YAL051W_mRNA	LN:3144
@SQ	SN:YAL049C_mRNA	LN:741
@SQ	SN:YAL048C_mRNA	LN:1989
@SQ	SN:YAL047W-A_mRNA	LN:330
@SQ	SN:YAL047C_mRNA	LN:1869
@SQ	SN:YAL046C_mRNA	LN:357
The folder sorted only contains 3 types BAM files per sample:
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genome.sorted.bam
transcriptome.sorted.bam
umi_dedup.transcriptome.bam
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I assume that the files in the folder deduplicated are supposed to be of the type `umi_dedup.transcriptome.bam`
j
Looks pretty conclusive, will just be a misplaced config element, will fix before I release
Thanks for testing!
f
awesome, thanks
these look consistent:
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for i in *umi_dedup.transcriptome.bam; do samtools view -H $i | wc -l; done                                        INT ✘  base   20:35:38
    7134
    7134
    7134
    7134
    7134
    7134
    7134
    7134
    7134
    7134
    7134
    7134
so do these:
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for i in *genome.sorted.bam; do samtools view -H $i | wc -l; done                                                      ✔  base   20:36:01
      24
      24
      24
      24
      24
      24
      24
      24
      24
      24
      24
      24
and the last ones:
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for i in *transcriptome.sorted.bam; do samtools view -H $i | wc -l; done                                               ✔  base   20:36:50
    7132
    7132
    7132
    7132
    7132
    7132
    7132
    7132
    7132
    7132
    7132
    7132
j
Hi Felix, I pushed some rationalisation of the config, the output looks sensible for me on testing, I only see 
*.umi_dedup.genome.sorted.bam
and 
*.transcriptome.sorted.bam
. Tbh I suspect I fixed this in earlier commits, but after you'd started testing, so the inappropriate files were just loitering in your output directory.
f
Hmm, I only did this processing yesterday (3 times), and deleted the output files on S3, then relaunched, but it might have been an older commit hash. JUst relaunched it once more, with pull_latest from. this branch
fingers crosssed
🤞 1
j
If problems recur, could you confirm the parameters you're using please?
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