Unconfigured Ad
Collapse
X
-
Try with a longer index, I think the recommended were between 12-14 long? 5 bases with no open positions does not make much sense for human. Masking strategies are described in the publications/documentations.
-
Solid-color space indexing for human fasta file
Hello,
I am using BFAST for indexing color space data using the command:
bfast index -f folder/human_bfast.fa -m '11111' -w 5 -A 1 -n 8
If I try to index the fasta file with a few chromosomes, say till 17, the tool successfully creates .bif file. But if I use a bigger fasta file (ie. from chr 1 till 22) for indexing then the tool throws error:
I want to create solid color space index for human fasta for all chromosomes from 1 through 22, X,YCurrently on [contig,pos]:
[------22,------662000]
Sorting by thread...
100.000 percent complete************************************************************
In function "RGIndexMergeHelperFromDiskContig_8": Fatal Error[ReadFileError]. Message: Could not read in tmp lower.
The file stream error was:: Bad file descriptor
***** Exiting due to errors *****
************************************************************
Please note that the step just prior to indexing (ie. creating reference in color space using the same fasta) was always successful. It creates .fa.cs.brg file successfully.
Can anybody please help me with the problem ?
Thanks in advance,
Aswathy
Latest Articles
Collapse
-
by SEQadmin2
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...-
Channel: Articles
10-14-2026, 09:55 AM -
-
by SEQadmin2
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...-
Channel: Articles
-
ad_right_rmr
Collapse
News
Collapse
| Topics | Statistics | Last Post | ||
|---|---|---|---|---|
|
Started by SEQadmin2, Yesterday, 11:13 AM
|
0 responses
21 views
0 reactions
|
Last Post
by SEQadmin2
Yesterday, 11:13 AM
|
||
|
Started by SEQadmin2, Yesterday, 10:48 AM
|
0 responses
18 views
0 reactions
|
Last Post
by SEQadmin2
Yesterday, 10:48 AM
|
||
|
Started by SEQadmin2, 10-15-2026, 10:52 AM
|
0 responses
36 views
0 reactions
|
Last Post
by SEQadmin2
10-15-2026, 10:52 AM
|
||
|
Started by SEQadmin2, 10-14-2026, 05:39 AM
|
0 responses
42 views
0 reactions
|
Last Post
by SEQadmin2
10-14-2026, 05:39 AM
|
Leave a comment: