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Search: Posts Made By: acoada
Forum: Bioinformatics 05-05-2014, 10:04 PM
Replies: 6
Views: 4,146
Posted By acoada
You're right. Samtools do sort while merging temp...

You're right. Samtools do sort while merging temp files, because there isn't ordinal order between temp files( each temp file contains all the chromosome... ) .
Forum: Bioinformatics 05-05-2014, 09:24 PM
Replies: 6
Views: 4,146
Posted By acoada
samtools has told me that [bam_sort_core]...

samtools has told me that
[bam_sort_core] merging from 630 files...
thus I am sure the all the temp files have been sorted and
samtools was killed while doing merging work ...

The point is,...
Forum: Bioinformatics 05-05-2014, 09:13 PM
Replies: 6
Views: 4,146
Posted By acoada
Yep, the total memory should under 20Gb, yet it...

Yep, the total memory should under 20Gb, yet it got 25Gb while merging, so it was killed.

I just wanna know is there any way to tell samtools to redo the merge( just the merge), 'cos the temp...
Forum: Bioinformatics 05-05-2014, 07:55 PM
Replies: 6
Views: 4,146
Posted By acoada
what if samtools sort failed while merging from temp files..

I was sorting a hug BAM file using
samtools sort -@ 5 -m 4G <in.bam> <out.prefix>

While merging from temp files
[bam_sort_core] merging from 630 files...
it was killed 'cos lack of memory......
Forum: Illumina/Solexa 12-30-2013, 07:06 PM
Replies: 6
Views: 10,831
Posted By acoada
try perl. you can store barcode list in a hash.

try perl.
you can store barcode list in a hash.
Forum: RNA Sequencing 12-26-2013, 10:27 PM
Replies: 1
Views: 1,764
Posted By acoada
Queistion about ArrayControl RNA spikes' sequence

Is there anybody knows the sequence of ArrayControl RNA spikes (Ambion, cat. no. AM1780)?

Here is the product page...
Forum: Illumina/Solexa 12-26-2013, 04:32 AM
Replies: 2
Views: 2,186
Posted By acoada
many thanks, but that's ERCC's sequences, not...

many thanks, but that's ERCC's sequences, not Ambion cat. No.AM1780

I do found the product page (http://www.lifetechnologies.com/order/catalog/product/AM1780?ICID=search-am1780), but the sequences...
Forum: Illumina/Solexa 12-26-2013, 12:19 AM
Replies: 2
Views: 2,186
Posted By acoada
Smile Question about SAMstrt Spike-in RNA

hi SEQers~
I recently read SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization on Bioinformatics, and failed to generate SAMseq-compatible...
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