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Search: Posts Made By: eilosei
Forum: Bioinformatics 05-11-2018, 12:08 PM
Replies: 4
Views: 2,309
Posted By eilosei
Here is my command: bwa sampe...

Here is my command:
bwa sampe RefGenome/mm9bwaidx file_1.bwa file_2.bwa file_1.fastq.gz file_2.fastq.gz > file.sam

This is the memory in my mac when I run the command.

Physical Memory: 16.00...
Forum: Bioinformatics 05-11-2018, 09:59 AM
Replies: 4
Views: 2,309
Posted By eilosei
Thank you for the suggestion. I tried to release...

Thank you for the suggestion. I tried to release the memory and hard drive space. The program processed a little bit more reads but it still stopped with the same error message. Is that because I...
Forum: Bioinformatics 05-10-2018, 08:50 AM
Replies: 4
Views: 2,309
Posted By eilosei
bwa samse problem

Hi there,

I'm trying to use bwa to align Paired-end reads to mouse genome. The alignment step goes well, but the bwa samse failed and generated error message like:

[bwa_sai2sam_pe_core] convert...
Forum: Bioinformatics 08-02-2012, 07:19 PM
Replies: 1
Views: 1,811
Posted By eilosei
Question problem with MarkDuplicates in Picard

Hi,

I tried to remove duplicates by Picard but got some problem. The command I used is

java -Xmx2g -Dsnappy.disable=true -jar ../picard-tools-1.70/MarkDuplicates.jar INPUT=file.sort.bam...
Forum: Illumina/Solexa 07-10-2012, 08:13 AM
Replies: 0
Views: 1,157
Posted By eilosei
PCR duplicates and reads mapping to multiple locations

Hi,

I have a ChIP-seq library built from Truseq kit. The alignment by BWA looks reasonable, with 14,826,606 out of 19,875,610 mapped to mouse genome. But only 6,504,252 left after removing...
Forum: General 06-11-2012, 02:31 PM
Replies: 0
Views: 974
Posted By eilosei
how to set up data range to show multiple sequence samples together?

Hi All,

I need to make a figure to display multiply sequence samples together in a genome browser view. My samples have different total reads (about 10 million, 30 million, and 100 million), how...
Forum: Bioinformatics 06-02-2012, 02:42 PM
Replies: 1
Views: 2,008
Posted By eilosei
CEAS gives incomplete result

Hi All,

I wish to usea CEAS to annotate the ChIP-seq peaks called from MACS. The command is:

ceas --name=file.ceas -g ../RefGenome/mm9.refGene -b file.macs_peaks.bed -w file.macs.wig.gz

But...
Forum: Bioinformatics 06-01-2012, 06:49 AM
Replies: 2
Views: 3,954
Posted By eilosei
Thank you! Now it works!

Thank you! Now it works!
Forum: Bioinformatics 05-31-2012, 08:29 PM
Replies: 2
Views: 3,954
Posted By eilosei
Question about MarkDuplicates.jar in Picard tool

Dear All,

I got an error when trying to remove duplicates in my sequence file with MarkDuplicates.jar in Picard tool.

Here is what I did:

I generated the alignment by BWA, then sorted the...
Forum: Bioinformatics 12-21-2011, 03:52 PM
Replies: 6
Views: 26,576
Posted By eilosei
Thank you for the suggestion. But the reheader...

Thank you for the suggestion. But the reheader command came out gibberish. What's the problem?


There is also the reheader command in samtools (http://samtools.sourceforge.net/samtools.shtml)

...
Forum: Bioinformatics 12-21-2011, 03:47 PM
Replies: 6
Views: 26,576
Posted By eilosei
This code works! Thank you!:)

This code works! Thank you!:)
Forum: Bioinformatics 12-19-2011, 03:33 PM
Replies: 6
Views: 26,576
Posted By eilosei
Question How to put header back to .bam file?

I've filtered my .bam file for uniquely mapped reads with this command:

samtools view file.bam | grep "XT:A:U" > file.unique.bam

Then I wish to convert the .unique.bam file to .bed file with...
Forum: Bioinformatics 12-14-2011, 09:27 PM
Replies: 4
Views: 4,423
Posted By eilosei
I tried to run MarkDuplicates.jar with the...

I tried to run MarkDuplicates.jar with the command

java -jar ./picard-tools-1.57/MarkDuplicates.jar METRICS_FILE=rmdup.txt INPUT=$file.bam OUTPUT=$file.rmdup.bam REMOVE_DUPLICATES=true

And got...
Forum: Bioinformatics 12-14-2011, 05:27 PM
Replies: 4
Views: 4,423
Posted By eilosei
Question how to install picard ?

Hi there,

I'm trying to use picard tools to remove duplicates from my sequence, but I'm having problem with installation. Has anyone installed picard-tools-1.57? Is there any detailed description...
Forum: Bioinformatics 12-14-2011, 05:11 PM
Replies: 2
Views: 3,156
Posted By eilosei
Unhappy Problem to use Bedtools after filtering uniquely mapped reads with samtools

Hi there,

I've aligned my ChIP-seq data with BWA and filtered for uniquely mapped reads with this command:

samtools view file.bam | grep "XT:A:U" > file.unique.bam

Then I tried to convert...
Forum: Illumina/Solexa 11-11-2011, 02:06 PM
Replies: 6
Views: 1,962
Posted By eilosei
Because the facility believed I gave them bad...

Because the facility believed I gave them bad samples, although they said no problem basing on the bioanalyzer result!:mad:
Forum: Illumina/Solexa 11-11-2011, 02:03 PM
Replies: 6
Views: 1,962
Posted By eilosei
Now the command works, and all my three samples...

Now the command works, and all my three samples from one lane have the same problem. The barcode of each read all carries a mismatch "N" at the second character, e.g. CNATGT, ANAGTG, GNCAAT.

I...
Forum: Illumina/Solexa 11-11-2011, 12:46 PM
Replies: 6
Views: 1,962
Posted By eilosei
Thank you for your quick reply. I tried the...

Thank you for your quick reply. I tried the command like

grep '@' 003_s_6_sequence.txt | cut -d '#' -f2 | sort |*uniq -c

But get the notice like

-bash: *uniq: command not found

Beside,...
Forum: Illumina/Solexa 11-11-2011, 10:28 AM
Replies: 6
Views: 1,962
Posted By eilosei
Unhappy Help! lost data in fastq file

I got some Illumina Hiseq result in fastq files from my facility, but the yield is a lot lower than expected.

For example, the summary file for one sample shows that it contains 225566 +/- 0...
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