Question: Unable to run Trans-ABySS on RNA_seq data?
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gravatar for sunnykevin97
9 weeks ago by
sunnykevin9750
sunnykevin9750 wrote:

I'm trying to run transabyss on RNA_Seq data obtained from Illumina Novaseq, says /home/data/brain_samples/fastqgz/10_S9_R1_001_trim.fastq:440: error: sequence with ID `A00943:16:HHMNGDRXX:1:2101:20609:1047/1' is empty make: * [transabyss-1.fa] Error

CMD

time transabyss --se /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq  --outdir /home/data/brain_samples/fastqgz/ --name 1_transabyssoutput  --threads 10 -k 32  > 1_transabyssoutput_log

Trim.fastq

grep -A3 'A00943:16:HHMNGDRXX:1:2101:20609:1047' head 10_S9_R1_001_trim.fastq

10_S9_R1_001_trim.fastq:@A00943:16:HHMNGDRXX:1:2101:20609:1047 1:N:0:CTGCTTCC+GATAGATC 10_S9_R1_001_trim.fastq- 10_S9_R1_001_trim.fastq-+ 10_S9_R1_001_trim.fastq-

Raw.fastq

grep -A3 'A00943:16:HHMNGDRXX:1:2101:20609:1047' head 10_S9_R1_001.fastq

10_S9_R1_001.fastq:@A00943:16:HHMNGDRXX:1:2101:20609:1047 1:N:0:CTGCTTCC+GATAGATC 10_S9_R1_001.fastqGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGCTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 10_S9_R1_001.fastq-+ 10_S9_R1_001.fastq-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFF:FFFF:FFF:FF::,:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF

comments!

rna-seq assembly • 101 views
ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 9 weeks ago by sunnykevin9750

Something is strange here:

10_S9_R1_001.fastq:@A00943:16:HHMNGDRXX:1:2101:20609:1047 1:N:0:CTGCTTCC+GATAGATC
10_S9_R1_001.fastq-
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGCTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

Why is the fastq header followed by this 10_S9_R1_001.fastq-

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax84k

10_S9_R1_001_trim.fastq:@A00943:16:HHMNGDRXX:1:2101:20609:1047 1:N:0:CTGCTTCC+GATAGATC 10_S9_R1_001_trim.fastq- 10_S9_R1_001_trim.fastq-+ 10_S9_R1_001_trim.fastq-

If this is what your fastq files look like then they are malformed. This could have happened during trimming which also seems to have left some 0 base pair (no sequence) reads. You will need to remove those by either redoing your trimming with a different program or filtering your currently files with reformat.sh minlen=10 (adjust the number as needed).

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax84k
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