Question: error in basespace qiime preprocessing
0
gravatar for nagpal511
12 months ago by
nagpal5110
nagpal5110 wrote:

Hi, we just had a 16S (V4) miseq-sequencing run per EMP protocol. The run went fine but when we try to process the samples on qiime preprocessing app, the summary sheet (produced by biom summarize-table) shows too low read count e.g. only 1 to 50 reads/sample. On the other hand, the summary produced by split_libraries_fastq.py in the same ppreprocessing run shows much higher reads/ sample e.g. over 50000 seq/ sample. Summarized table and one sample (RN) details are pasted below. Plz note the 94017 sequence in this sample vs. only 30.0 in the summary over it. We've been doing this for long time without ever facing such error; and we used same protocol, barcodes and library prep methods this time too, so don't really know where's the problem. We cannot proceed to qiime visualization without fixing this problem. Could anyone please help in resolving this? Will be highly grateful for help. Many thanks in advance!

Summary produced by biom summarize-table

Num samples: 7
Num observations: 38
Total count: 150
Table density (fraction of non-zero values): 0.195

Counts/sample summary:

Min: 4.0
Max: 39.0
Median: 28.000
Mean: 21.429
Std. dev.: 12.960
Sample Metadata Categories: None provided
Observation Metadata Categories: taxonomy

Counts/sample detail:

B6Old78wk3: 4.0
B6Old78wk2: 8.0
B6Old78wk1: 9.0
B6Young4wk3: 28.0
RN: 30.0
B6Young4wk1: 32.0
B6Young4wk2: 39.0
Summary produced by split_libraries_fastq.py
Input file paths
Sequence read filepath: /data/input/samples/115162121/RN_S191_L001_R1_001.fastq.gz (md5: 8f40789c606c389722dc770ef4b3939f)
Quality filter results
Total number of input sequences: 94104
Barcode not in mapping file: 0
Read too short after quality truncation: 61
Count of N characters exceeds limit: 26
Illumina quality digit = 0: 0
Barcode errors exceed max: 0

Result summary (after quality filtering)

Median sequence length: 300.00
RN  94017

Total number seqs written   94017
---
ADD COMMENTlink modified 11 months ago by Kevin Blighe39k • written 12 months ago by nagpal5110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1608 users visited in the last hour