Hi,
Would it be possible to have the original Drop-Seq Bam file?
Thank you
Created by Marouen Hi @nukappa ,
It was my mistake; I have not used proper argument with "fastq-dump" program from "sra-toolkit" to extract the fasta files from GEO.
However should not QUALITY_FORMAT be Illumina , the sequencing platform??
Thanks for replying,
Rishi
From the error output it seems that the "QUALITY_FORMAT" is not recognized. What is the default value there? Does it maybe work if you uncompress the files? Hello,
I have downloaded the raw fastq files from GEO and was trying to follow the data-processing as described in the supplementary text of main article.
However an error was generated when following command was executed to generate unaligned bam file.
```
picard FastqToSam FASTQ2=sra_fastq/SRR5269562.fastq.gz FASTQ=sra_fastq/SRR5269563.fastq.gz QUALITY_FORMAT=Illumina OUTPUT=SAMN06344991.bam SAMPLE_NAME=MS_Sample17 SORT_ORDER=queryname
```
The error was
```
[Mon Oct 08 07:25:47 GMT 2018] FastqToSam FASTQ=sra_fastq/SRR5269563.fastq.gz FASTQ2=sra_fastq/SRR5269562.fastq.gz QUALITY_FORMAT=Illumina OUTPUT=SAMN06344991.bam SAMPLE_NAME=MS_Sample17 SORT_ORDER=queryname USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon Oct 08 07:25:47 GMT 2018] Executing as dasroy@c951 on Linux 2.6.32-642.15.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_151-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.10-SNAPSHOT
[Mon Oct 08 07:25:47 GMT 2018] picard.sam.FastqToSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2045509632
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: The quality values do not fall in the range appropriate for the expected quality of Illumina.
at htsjdk.samtools.util.QualityEncodingDetector.generateBestGuess(QualityEncodingDetector.java:378)
at picard.sam.FastqToSam.determineQualityFormat(FastqToSam.java:244)
at picard.sam.FastqToSam.doWork(FastqToSam.java:316)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
```
Please let me know how to fix this problem.
With regards
Rishi Thanks! The raw data are available through the associated GEO submission
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95025
You'd have to process the .fastq files to get to the .bam files though.
Drop files to upload
Is it possible to get the original data? page is loading…