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Search: Posts Made By: shimingt
Forum: Bioinformatics 01-30-2019, 07:48 PM
Replies: 104
Views: 46,817
Posted By shimingt
Hello there, I am running into an error...

Hello there,

I am running into an error whenever I tried to run Tadpole:

Performing error-correction with Tadpole

java -ea -Xmx117184m -Xms117184m -cp...
Forum: Bioinformatics 12-04-2018, 05:01 PM
Replies: 57
Views: 53,948
Posted By shimingt
Hello there, I have performed a metagenomics...

Hello there,

I have performed a metagenomics sequencing on my samples on an Illumina Hi-Seq. How do I determine the target coverage value to use?

Thanks in advance.
Forum: Bioinformatics 02-21-2017, 04:47 PM
Replies: 693
Views: 243,467
Posted By shimingt
Dear Brian, Thanks for your reply. ...

Dear Brian,

Thanks for your reply.

This is from one of the mapping files (.csv) for mmgenome.

tanshiming@S620100019205:~/Downloads$ head C13.11.14.csv
"Name","Consensus length","Total...
Forum: Bioinformatics 02-19-2017, 08:20 PM
Replies: 693
Views: 243,467
Posted By shimingt
Converting a coverage file into a csv format for mmgenome

Hello there,

Is there a way I could convert the mapping files that bbmap produced into csv coverage file that can be used for the mmgenome software (link:...
Forum: Bioinformatics 02-08-2017, 01:06 AM
Replies: 693
Views: 243,467
Posted By shimingt
Difficulties using bbmap to generate sorted, indexed bam file

Hello people,

I am trying to generate sorted, indexed bam file with the bbmap tool, but I have an error message.

tanshiming@S620100019205:~/Documents/ACDC-trial/shimingles$ bbmap.sh...
Forum: Bioinformatics 06-16-2016, 12:45 AM
Replies: 132
Views: 82,653
Posted By shimingt
Dear Genomax, Thanks for your help!

Dear Genomax,

Thanks for your help!
Forum: Bioinformatics 06-14-2016, 05:31 PM
Replies: 132
Views: 82,653
Posted By shimingt
Log file from bbmerge

Hello GenoMax,

Thanks for your reply.

I tried a command like this:

for x in *_R1_001.fastq;do echo bbmerge.sh -Xmx20g in1=$x in2=${x%_R1_001.*}_R2_001.fastq...
Forum: Bioinformatics 06-14-2016, 03:30 AM
Replies: 132
Views: 82,653
Posted By shimingt
Log File

Hello,

I am a novice with command prompt. I can't seem to get a log file.

This is my command prompt:

for x in *_R1_001.fastq;do echo bbmerge.sh -Xmx20g in1=$x in2=${x%_R1_001.*}_R2_001.fastq...
Forum: Bioinformatics 06-14-2016, 01:30 AM
Replies: 132
Views: 82,653
Posted By shimingt
Hello there! Is there a way we could generate a...

Hello there! Is there a way we could generate a stats or log file with bbmerge?
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