j*p
2 楼
sra 可以换bam吗？我只知道sra to fastq
l*1
3 楼
同意楼下的
Step one
SRAto fastq
btw LZ be careful:
cited:
The problem you are experiencing is that the version of the SRA toolkit is
out of date and that there is now an un(der)documented option in fastq-dump
to dump paired end data from an SRA-lite submission. The guidance notes on
the NCBI website you refer to are for version 2.0.1, and state that they are
not up to date:
link:
//www.biostars.org/post/show/11111/how-to-convert-sra-lite-paired-end-
submission-to-fastq/
then try
FASTQ to BAM (version 1.56.0)
by tool:
httpS//test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
Step one
SRAto fastq
btw LZ be careful:
cited:
The problem you are experiencing is that the version of the SRA toolkit is
out of date and that there is now an un(der)documented option in fastq-dump
to dump paired end data from an SRA-lite submission. The guidance notes on
the NCBI website you refer to are for version 2.0.1, and state that they are
not up to date:
link:
//www.biostars.org/post/show/11111/how-to-convert-sra-lite-paired-end-
submission-to-fastq/
then try
FASTQ to BAM (version 1.56.0)
by tool:
httpS//test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
n*7
4 楼
fastq怎么可以到bam呢？
需要align啊
或者直接转成unaligned的？这个不是多此一举吗
dump
are
【在 l**********1 的大作中提到】
: 同意楼下的
: Step one
: SRAto fastq
: btw LZ be careful:
: cited:
: The problem you are experiencing is that the version of the SRA toolkit is
: out of date and that there is now an un(der)documented option in fastq-dump
: to dump paired end data from an SRA-lite submission. The guidance notes on
: the NCBI website you refer to are for version 2.0.1, and state that they are
: not up to date:
需要align啊
或者直接转成unaligned的？这个不是多此一举吗
dump
are
【在 l**********1 的大作中提到】
: 同意楼下的
: Step one
: SRAto fastq
: btw LZ be careful:
: cited:
: The problem you are experiencing is that the version of the SRA toolkit is
: out of date and that there is now an un(der)documented option in fastq-dump
: to dump paired end data from an SRA-lite submission. The guidance notes on
: the NCBI website you refer to are for version 2.0.1, and state that they are
: not up to date:
w*w
5 楼
新的sra toolkit里已经有一个sam-dump工具,跑10G以下的小文件没什么问题，100G以
上的，跑一个2，3个礼拜还可以接受。同时跑两个，performance马上不行，要20，30
个礼拜才能完成。
上的，跑一个2，3个礼拜还可以接受。同时跑两个，performance马上不行，要20，30
个礼拜才能完成。
w*w
6 楼
傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
的是好几个大文件都出错了。
的是好几个大文件都出错了。
j*p
7 楼
still did not get LZ's point. but whatever.
l*1
8 楼
最新 plus 正版吗 那个soft?
Sam≂BAM format
pls refer:
What 'Picard' does?
FastqToSam converts FASTQ files to unaligned BAM files.
httPS://test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
【在 w****w 的大作中提到】
: 傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
: 的是好几个大文件都出错了。
Sam≂BAM format
pls refer:
What 'Picard' does?
FastqToSam converts FASTQ files to unaligned BAM files.
httPS://test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
【在 w****w 的大作中提到】
: 傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
: 的是好几个大文件都出错了。
s*s
9 楼
I think you mean cSRA to BAM? SRA to BAM 没有意义啊
w*w
10 楼
我拿到的文件应该都是cSRA,虽然都是sra extension.
【在 s******s 的大作中提到】
: I think you mean cSRA to BAM? SRA to BAM 没有意义啊
【在 s******s 的大作中提到】
: I think you mean cSRA to BAM? SRA to BAM 没有意义啊
w*w
11 楼
原来以为只能用samtools从bam文件抽取区域，得把整个cSRA先转成bam,计算量会太大
。后来发现sam-dump有--aligned-region option,问题就解决了。
【在 j*p 的大作中提到】
: still did not get LZ's point. but whatever.
。后来发现sam-dump有--aligned-region option,问题就解决了。
【在 j*p 的大作中提到】
: still did not get LZ's point. but whatever.
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